Length (hg19) : 2,903,920 bases - Length (hg38) : 2,537,144 bases


skin eye ear brain/cognition face skeleton skin skin musculature skin skin skin skin skin skin

CNV-Hub AChro-Puce
Pathogenic



AChro-Puce Criteria taken into account 1

Class

2 Major

CNV inherited from Asymptomatic parent

Class

2 Minor

At least 1 occurrence in DGV / DGV-Gold > 50 % overlaps

Class

4 Major

De novo CNV or inherited from Symptomatic parent

Class

4 Major

At least one occurrence in patients databases as pathogenic or likely pathogenic

Class

4 Major

Haploinsufficient gene

Class

4 Minor

CNV more frequent in Coe & Al patient cases than in controls

Class

4 Minor

At least one occurrence in patients databases as pathogenic or likely pathogenic > 50 % overlaps

Class

4 Minor

CNV length of 1 Mb or more

Class

5 

Deletion, Duplication, Microdeletion or Microduplication syndrome detected : 22q11.2 deletion syndrome | Distal 22q11.2 microdeletion syndrome.


ISV 2

XCNV 3

ClassifyCNV ACMG 4

AnnotSV ACMG 5

ACMG criteria

ClassifyCNV

2A
+ 1

Complete overlap of an established HI gene/genomic region.

2H
+ 0.15

Multiple HI predictors suggest that AT LEAST ONE gene in the interval is haploinsufficient (HI).

3C
+ 0.9

Number of protein-coding RefSeq genes wholly or partially included in the CNV region.

5B
-0.45

Patient with specific, well-defined phenotype and no family history. CNV is inherited from an apparently unaffected parent.

5D
+ 0.45

CNV segregates with a consistent phenotype observed in the patient’s family.

AnnotSV

2A
+ 1

Complete overlap of an established HI gene/genomic region.

3C
+ 0.9

Number of protein-coding RefSeq genes wholly or partially included in the CNV region.

5B
-0.45

Patient with specific, well-defined phenotype and no family history. CNV is inherited from an apparently unaffected parent.

5D
+ 0.45

CNV segregates with a consistent phenotype observed in the patient’s family.


Microdeletion syndromes

70 % Overlaps
Name Start End Overlaps Link
22q11 deletion syndrome (Velocardiofacial / DiGeorge syndrome) 19022279 21098156
Coverage of CNV on syndrome : 83 %
Decipher
DIGEORGE SYNDROME; DGS 19022279 21098156
Coverage of CNV on syndrome : 83 %
DecipherGenomics

Diseases :

Gene Disease Source Inheritance
HIRA 22q11.2 deletion syndrome Orphanet Autosomal dominant
UFD1 22q11.2 deletion syndrome Orphanet Autosomal dominant
TBX1 22q11.2 deletion syndrome Orphanet Autosomal dominant
ARVCF 22q11.2 deletion syndrome Orphanet Autosomal dominant
CRKL Distal 22q11.2 microdeletion syndrome Orphanet Autosomal dominant
LZTR1 Schwannomatosis Orphanet Autosomal dominant
SLC25A1 Presynaptic congenital myasthenic syndromes Orphanet Autosomal dominant, Autosomal recessive
CDC45 Ear-patella-short stature syndrome Orphanet Autosomal dominant, Autosomal recessive
PRODH Hyperprolinemia type 1 Orphanet Autosomal recessive
CLTCL1 Congenital insensitivity to pain with severe intellectual disability Orphanet Autosomal recessive
TXNRD2 Familial glucocorticoid deficiency Orphanet Autosomal recessive
SCARF2 Van den Ende-Gupta syndrome Orphanet Autosomal recessive
SNAP29 CEDNIK syndrome Orphanet Autosomal recessive
GP1BB Fetal and neonatal alloimmune thrombocytopenia Orphanet Not applicable
CLDN5 cldn5-related neurodevelopmental disorder DDG2P
TANGO2 Recurrent metabolic encephalomyopathic crises-rhabdomyolysis-cardiac arrhythmia-intellectual disability syndrome Orphanet
PI4KA Bilateral perisylvian polymicrogyria Orphanet

ClinGen

0 benign CNV
0 likely benign CNV
0 uncertain CNV
4 likely pathogenic CNV
172 pathogenic CNV

70% Overlaps


Decipher

0 benign CNV
118 unknown CNV
11 uncertain CNV
118 pathogenic CNV

70% Overlaps

DGV-Gold

0

80% Overlaps

0

50% Overlaps


DGV

0

80% Overlaps

1

50% Overlaps


Coe & Al study 6

17

Patient cases
70% Overlaps

0

Controls
70% Overlaps


Genes with pHaplo > 0.55 7

11

HIRA CLDN5 TBX1 DGCR8 RTN4R SCARF2 MED15 PI4KA SERPIND1 CRKL HIC2

Genes with pTriplo > 0.68 7

12

HIRA TBX1 DGCR8 RANBP1 SCARF2 KLHL22 MED15 PI4KA CRKL THAP7 HIC2

Genes in SFARI

5

PRODH CLTCL1 TBX1 GNB1L LZTR1

Genes in OMIM

45


Sources and references

1 : AChroPuce Consortium Recommandations pour l’interpretation Clinique des CNV (Copy Number Variations) Septembre 2022.

2 : Automated prediction of the clinical impact of structural copy number variations : M. Gažiová, T. Sládeček, O. Pös, M. Števko, W. Krampl, Z. Pös, R. Hekel, M. Hlavačka, M. Kucharík, J. Radvánszky, J. Budiš & T. Szemes View article

3 : Zhang L, Shi J, Ouyang J, Zhang R, Tao Y, Yuan D, et al X CNV genome wide prediction of the pathogenicity of copy number variations Genome Med 2021 13 132.

4 : Gurbich, T.A., Ilinsky, V.V. ClassifyCNV: a tool for clinical annotation of copy-number variants. Sci Rep 10, 20375 (2020). View article

5 : Geoffroy V, Herenger Y, Kress A, et al. AnnotSV: an integrated tool for structural variations annotation. Bioinforma Oxf Engl. 2018;34(20):3572-3574. doi:10.1093/bioinformatics/bty304

6 : Coe BP, Witherspoon K, Rosenfeld JA, van Bon BWM, Vulto van Silfhout AT, Bosco P, et al Refining analyses of copy number variation identifies specific genes associated with developmental delay Nat Genet 2014 46 1063 71

7 : Collins RL, Glessner JT, Porcu E, Lepamets M, Brandon R, Lauricella C, et al A cross disorder dosage sensitivity map of the human genome Cell 2022 185 3041 3055 e 25

Not Working? You Can Delete and Recompute the CNV

2 Microdeletion and microduplication syndromes from litterature (>= 70% only)

DGS/VCFS AC (22q11.2)
Location : 18,832,752 - 21,047,287 | Size : 2,214,535 bases

Cases :
Burnside_2015
Morrow_2018
Mean Coverage : 84 %


DGS/VCFS AD (22q11.2)
Location : 18,912,231 - 21,465,672 | Size : 2,553,441 bases

Cases :
Gottlieb_1998
McDermid_2002
Kaminsky_2011
Burnside_2015
Morrow_2018
Mean Coverage : 94 %



45 OMIM Gene overlap(s)

Download genes as .csv

PI4KA NM_058004.4   Whole gene - Size : 151,726 bases


pLI : 0 LOEUF : 0.46 sHet : 0.015 pHaplo : 0.69 pTriplo : 0.84
Location : 21,061,979 - 21,213,705

Disease : Bilateral perisylvian polymicrogyria

Source : Orphanet

Database :

DecipherGenomics PanelApp OMIM:600286 Orphanet:98889 HGNC:8983 PMID:25855803 GTEx Portal Human Protein Atlas Ensembl

HIRA NM_003325.4   Whole gene - Size : 116,752 bases

brain/cognition

pLI : 1 LOEUF : 0.14 sHet : 0.38 pHaplo : 0.92 pTriplo : 0.99
Location : 19,318,221 - 19,434,973

Disease : 22q11.2 deletion syndrome

Source : Orphanet

Database :

DecipherGenomics PanelApp OMIM:600237 Orphanet:567 HGNC:4916 PMID:15177686 GTEx Portal Human Protein Atlas Ensembl

CLTCL1 NM_007098.4   Whole gene - Size : 112,256 bases


pLI : 0 LOEUF : 0.99 sHet : 0.007 pHaplo : 0.11 pTriplo : 0.35
Location : 19,166,986 - 19,279,242

Disease : Congenital insensitivity to pain with severe intellectual disability

Source : Orphanet

Database :

DecipherGenomics PanelApp OMIM:601273 Orphanet:453510 HGNC:2093 PMID:26068709 GTEx Portal Human Protein Atlas Ensembl


SFARI (Autism Database) :

Gene Score : 2
Is Not Syndromic
No EAGLE Score
Reports : 6

MED15 NM_001003891.3   Whole gene - Size : 91,719 bases


pLI : 1 LOEUF : 0.24 sHet : 0.101 pHaplo : 0.81 pTriplo : 0.97
Location : 20,850,200 - 20,941,919

Database :

DecipherGenomics OMIM:607372 GTEx Portal Human Protein Atlas Ensembl

DGCR2 NM_005137.3   Whole gene - Size : 86,172 bases


pLI : 0 LOEUF : 0.88 sHet : 0.017 pHaplo : 0.13 pTriplo : 0.58
Location : 19,023,795 - 19,109,967

Database :

DecipherGenomics OMIM:600594 GTEx Portal Human Protein Atlas Ensembl

GNB1L NM_053004.3   Whole gene - Size : 71,716 bases


pLI : 0 LOEUF : 1.05 sHet : 0.005 pHaplo : 0.04 pTriplo : 0.25
Location : 19,770,746 - 19,842,462

Database :

DecipherGenomics PanelApp OMIM:610778 GTEx Portal Human Protein Atlas Ensembl


SFARI (Autism Database) :

Gene Score : 2
Is Not Syndromic
No EAGLE Score
Reports : 2

TXNRD2 NM_006440.5   Whole gene - Size : 66,303 bases


pLI : 0 LOEUF : 0.99 sHet : 0.004 pHaplo : 0.07 pTriplo : 0.43
Location : 19,863,040 - 19,929,343

Disease : Familial glucocorticoid deficiency

Source : Orphanet

Database :

DecipherGenomics PanelApp OMIM:606448 Orphanet:361 HGNC:18155 PMID:24601690 GTEx Portal Human Protein Atlas Ensembl

DGCR5 -   Whole gene - Size : 60,803 bases



Location : 18,957,952 - 19,018,755

Database :

DecipherGenomics OMIM:618040 GTEx Portal Human Protein Atlas Ensembl

KLHL22 NM_032775.4   Whole gene - Size : 54,325 bases


pLI : 0.42 LOEUF : 0.44 sHet : 0.026 pHaplo : 0.48 pTriplo : 0.79
Location : 20,795,806 - 20,850,131

Database :

DecipherGenomics OMIM:618020 GTEx Portal Human Protein Atlas Ensembl

TANGO2 NM_152906.7   Whole gene - Size : 50,150 bases

brain/cognition musculature

pLI : 0 LOEUF : 0.89 sHet : 0.007 pHaplo : 0.04 pTriplo : 0.44
Location : 20,004,537 - 20,054,687

Disease : Recurrent metabolic encephalomyopathic crises-rhabdomyolysis-cardiac arrhythmia-intellectual disability syndrome

Source : Orphanet

Database :

DecipherGenomics PanelApp OMIM:616830 Orphanet:480864 HGNC:25439 PMID:26805782 GTEx Portal Human Protein Atlas Ensembl

ARVCF NM_001670.3   Whole gene - Size : 46,927 bases


pLI : 0 LOEUF : 0.82 sHet : 0.005 pHaplo : 0.17 pTriplo : 0.39
Location : 19,957,419 - 20,004,346

Disease : 22q11.2 deletion syndrome

Source : Orphanet

Database :

DecipherGenomics PanelApp OMIM:602269 Orphanet:567 HGNC:728 GTEx Portal Human Protein Atlas Ensembl

RTN4R NM_023004.6   Whole gene - Size : 41,831 bases


pLI : 0.96 LOEUF : 0.3 pHaplo : 0.63 pTriplo : 0.59
Location : 20,228,938 - 20,270,769

Database :

DecipherGenomics OMIM:605566 GTEx Portal Human Protein Atlas Ensembl

CDC45 NM_003504.5   Whole gene - Size : 41,155 bases

ear brain/cognition skeleton

pLI : 0 LOEUF : 0.58 sHet : 0.018 pHaplo : 0.17 pTriplo : 0.25
Location : 19,466,980 - 19,508,135

Disease : Ear-patella-short stature syndrome

Source : Orphanet

Database :

DecipherGenomics PanelApp OMIM:603465 Orphanet:2554 HGNC:1739 PMID:27374770 GTEx Portal Human Protein Atlas Ensembl

CRKL NM_005207.4   Whole gene - Size : 36,340 bases


pLI : 0.45 LOEUF : 0.64 sHet : 0.03 pHaplo : 0.67 pTriplo : 0.94
Location : 21,271,695 - 21,308,035

Disease : Distal 22q11.2 microdeletion syndrome

Source : Orphanet

Database :

DecipherGenomics PanelApp OMIM:602007 Orphanet:261330 HGNC:2363 GTEx Portal Human Protein Atlas Ensembl

HIC2 NM_015094.3   Exons: 1->2 / 3 - Size : 34,092 bases


pLI : 1 LOEUF : 0.18 sHet : 0.178 pHaplo : 0.8 pTriplo : 0.94
Location : 21,771,660 - 21,805,752

Database :

DecipherGenomics OMIM:607712 GTEx Portal Human Protein Atlas Ensembl

SNAP29 NM_004782.4   Whole gene - Size : 32,207 bases

eye brain/cognition face

pLI : 0.01 LOEUF : 0.86 sHet : 0.019 pHaplo : 0.26 pTriplo : 0.3
Location : 21,213,295 - 21,245,502

Disease : CEDNIK syndrome

Source : Orphanet

Database :

DecipherGenomics PanelApp OMIM:604202 Orphanet:66631 HGNC:11133 PMID:15968592 PMID:2107345 GTEx Portal Human Protein Atlas Ensembl

DGCR8 NM_022720.7   Whole gene - Size : 31,656 bases


pLI : 1 LOEUF : 0.21 sHet : 0.303 pHaplo : 0.8 pTriplo : 1
Location : 20,067,744 - 20,099,400

Database :

DecipherGenomics PanelApp OMIM:609030 GTEx Portal Human Protein Atlas Ensembl

UFD1 NM_005659.7   Whole gene - Size : 29,291 bases


pLI : 1 LOEUF : 0.23
Location : 19,437,434 - 19,466,725

Disease : 22q11.2 deletion syndrome

Source : Orphanet

Database :

DecipherGenomics OMIM:601754 Orphanet:567 HGNC:12520 GTEx Portal Human Protein Atlas Ensembl

TBX1 NM_001379200.1   Whole gene - Size : 26,890 bases

brain/cognition

pLI : 0.84 LOEUF : 0.43 sHet : 0.195 pHaplo : 0.85 pTriplo : 0.72
Location : 19,744,226 - 19,771,116

Disease : 22q11.2 deletion syndrome

Source : Orphanet

Database :

DecipherGenomics PanelApp OMIM:602054 Orphanet:567 HGNC:11592 GTEx Portal Human Protein Atlas Ensembl


SFARI (Autism Database) :

No Gene Score
Is Syndromic
No EAGLE Score
Reports : 5

PRODH NM_016335.6   Whole gene - Size : 23,776 bases


pLI : 0 LOEUF : 1.1 pHaplo : 0.39 pTriplo : 0.53
Location : 18,900,290 - 18,924,066

Disease : Hyperprolinemia type 1

Source : Orphanet

Database :

DecipherGenomics PanelApp OMIM:606810 Orphanet:419 HGNC:9453 PMID:20524212 PMID:234626 GTEx Portal Human Protein Atlas Ensembl


SFARI (Autism Database) :

Gene Score : 2
Is Syndromic
No EAGLE Score
Reports : 6

ZDHHC8 NM_013373.4   Whole gene - Size : 18,551 bases


pLI : 0.85 LOEUF : 0.37 sHet : 0.305 pHaplo : 0.32 pTriplo : 0.68
Location : 20,116,979 - 20,135,530

Database :

DecipherGenomics OMIM:608784 GTEx Portal Human Protein Atlas Ensembl

P2RX6 NM_005446.5   Whole gene - Size : 18,205 bases


pLI : 0 LOEUF : 1.1 pHaplo : 0.11 pTriplo : 0.36
Location : 21,364,097 - 21,382,302

Database :

DecipherGenomics OMIM:608077 GTEx Portal Human Protein Atlas Ensembl

GGT2P -   Whole gene - Size : 17,581 bases



Location : 21,562,262 - 21,579,843

Database :

DecipherGenomics OMIM:137181 GTEx Portal Human Protein Atlas Ensembl

LZTR1 NM_006767.4   Whole gene - Size : 16,763 bases


pLI : 0 LOEUF : 1.98 sHet : 0.004 pHaplo : 0.16 pTriplo : 0.4
Location : 21,336,558 - 21,353,321

Disease : Schwannomatosis

Source : Orphanet

Database :

DecipherGenomics PanelApp OMIM:600574 Orphanet:93921 HGNC:6742 PMID:24362817 GTEx Portal Human Protein Atlas Ensembl


SFARI (Autism Database) :

Gene Score : 1
Is Not Syndromic
No EAGLE Score
Reports : 14

AIFM3 NM_001386814.1   Whole gene - Size : 16,253 bases


pLI : 0 LOEUF : 0.99 sHet : 0.004 pHaplo : 0.15 pTriplo : 0.5
Location : 21,319,396 - 21,335,649

Database :

DecipherGenomics OMIM:617298 GTEx Portal Human Protein Atlas Ensembl

ESS2 NM_022719.3   Whole gene - Size : 14,405 bases


pLI : 0 LOEUF : 0.96
Location : 19,117,792 - 19,132,197

Database :

DecipherGenomics OMIM:601755 GTEx Portal Human Protein Atlas Ensembl

ZNF74 NM_003426.4   Whole gene - Size : 14,346 bases


pLI : 0 LOEUF : 0.89 sHet : 0.008 pHaplo : 0.2 pTriplo : 0.37
Location : 20,748,405 - 20,762,751

Database :

DecipherGenomics OMIM:194548 GTEx Portal Human Protein Atlas Ensembl

SERPIND1 NM_000185.4   Whole gene - Size : 13,607 bases


pLI : 0 LOEUF : 1.5 sHet : 0.01 pHaplo : 0.61 pTriplo : 0.41
Location : 21,128,401 - 21,142,008

Database :

DecipherGenomics PanelApp OMIM:142360 GTEx Portal Human Protein Atlas Ensembl

SCARF2 NM_182895.5   Whole gene - Size : 13,239 bases

skin skeleton

pHaplo : 0.95 pTriplo : 0.81
Location : 20,778,874 - 20,792,113

Disease : Van den Ende-Gupta syndrome

Source : Orphanet

Database :

DecipherGenomics PanelApp OMIM:613619 Orphanet:2460 HGNC:19869 PMID:20887961 PMID:2214038 GTEx Portal Human Protein Atlas Ensembl

RANBP1 NM_001278639.2   Whole gene - Size : 11,417 bases


pLI : 0.63 LOEUF : 0.93 sHet : 0.154 pHaplo : 0.39 pTriplo : 0.93
Location : 20,103,461 - 20,114,878

Database :

DecipherGenomics OMIM:601180 GTEx Portal Human Protein Atlas Ensembl

SEPTIN5 NM_002688.6   Whole gene - Size : 9,721 bases


pLI : 0.93 LOEUF : 0.36
Location : 19,702,026 - 19,711,747

Database :

DecipherGenomics OMIM:602724 GTEx Portal Human Protein Atlas Ensembl

DGCR6 NM_005675.6   Exons: 3->5 / 5 - Size : 8,210 bases


pLI : 0 LOEUF : 1.83 pHaplo : 0.2 pTriplo : 0.52
Location : 18,893,541 - 18,901,751

Database :

DecipherGenomics OMIM:601279 GTEx Portal Human Protein Atlas Ensembl

RIMBP3 NM_015672.2   Whole gene - Size : 6,104 bases


pHaplo : 0.1 pTriplo : 0.34
Location : 20,455,682 - 20,461,786

Database :

DecipherGenomics OMIM:612699 GTEx Portal Human Protein Atlas Ensembl

DGCR6L NM_033257.4   Whole gene - Size : 5,842 bases


pLI : 0 LOEUF : 1.27 sHet : 0.024 pHaplo : 0.07 pTriplo : 0.34
Location : 20,301,761 - 20,307,603

Database :

DecipherGenomics OMIM:609459 GTEx Portal Human Protein Atlas Ensembl

RIMBP3B NM_001128635.2   Whole gene - Size : 5,727 bases


pHaplo : 0.13 pTriplo : 0.27
Location : 21,738,040 - 21,743,767

Database :

DecipherGenomics OMIM:612700 GTEx Portal Human Protein Atlas Ensembl

TRMT2A NM_022727.6   Whole gene - Size : 5,517 bases


pLI : 0 LOEUF : 0.92 sHet : 0.018 pHaplo : 0.28 pTriplo : 0.67
Location : 20,099,398 - 20,104,915

Database :

DecipherGenomics OMIM:611151 GTEx Portal Human Protein Atlas Ensembl

CLDN5 NM_001363066.2   Whole gene - Size : 4,521 bases


pLI : 0.9 LOEUF : 0.41 pHaplo : 0.68 pTriplo : 0.6
Location : 19,510,547 - 19,515,068

Disease : cldn5-related neurodevelopmental disorder

Source : DDG2P

Database :

DecipherGenomics PanelApp OMIM:602101 GTEx Portal Human Protein Atlas Ensembl

SLC7A4 NM_004173.3   Whole gene - Size : 4,122 bases


pLI : 0 LOEUF : 1.23 sHet : 0.004 pHaplo : 0.2 pTriplo : 0.34
Location : 21,383,007 - 21,387,129

Database :

DecipherGenomics OMIM:603752 GTEx Portal Human Protein Atlas Ensembl

MRPL40 NM_003776.4   Whole gene - Size : 3,530 bases


pLI : 0.05 LOEUF : 0.79 sHet : 0.014 pHaplo : 0.24 pTriplo : 0.48
Location : 19,420,068 - 19,423,598

Database :

DecipherGenomics PanelApp OMIM:605089 GTEx Portal Human Protein Atlas Ensembl

GSC2 NM_005315.2   Whole gene - Size : 3,299 bases


pLI : 0 LOEUF : 1.91 pHaplo : 0.41 pTriplo : 0.08
Location : 19,134,506 - 19,137,805

Database :

DecipherGenomics OMIM:601845 GTEx Portal Human Protein Atlas Ensembl

SLC25A1 NM_005984.5   Whole gene - Size : 3,158 bases

brain/cognition

pLI : 0.06 LOEUF : 0.65 sHet : 0.065 pHaplo : 0.09 pTriplo : 0.38
Location : 19,163,094 - 19,166,252

Disease : Presynaptic congenital myasthenic syndromes

Source : Orphanet

Database :

DecipherGenomics PanelApp OMIM:190315 Orphanet:98914 HGNC:10979 GTEx Portal Human Protein Atlas Ensembl

THAP7 NM_030573.3   Whole gene - Size : 3,092 bases


pLI : 0.01 LOEUF : 0.86 sHet : 0.057 pHaplo : 0.37 pTriplo : 0.73
Location : 21,353,393 - 21,356,485

Database :

DecipherGenomics OMIM:609518 GTEx Portal Human Protein Atlas Ensembl

GGTLC3 NM_001355479.1   Whole gene - Size : 1,817 bases


pHaplo : 0.06 pTriplo : 0.43
Location : 20,366,211 - 20,368,028

Database :

DecipherGenomics OMIM:612340 GTEx Portal Human Protein Atlas Ensembl

TSSK2 NM_053006.5   Whole gene - Size : 1,314 bases


pLI : 0 LOEUF : 1.15 sHet : 0.009 pHaplo : 0.23 pTriplo : 0.36
Location : 19,118,821 - 19,120,135

Database :

DecipherGenomics OMIM:610710 GTEx Portal Human Protein Atlas Ensembl

GP1BB NM_000407.5   Whole gene - Size : 1,232 bases


pLI : 0.51 LOEUF : 1.33 pHaplo : 0.25 pTriplo : 0.53
Location : 19,711,062 - 19,712,294

Disease : Fetal and neonatal alloimmune thrombocytopenia

Source : Orphanet

Database :

DecipherGenomics PanelApp OMIM:138720 Orphanet:853 HGNC:4440 GTEx Portal Human Protein Atlas Ensembl


142 Non-OMIM Gene overlap(s)

C22orf39
Size : 96,343 bases

pLI : 0 LOEUF : 1.77 pHaplo : 0.09 pTriplo : 0.31
Location : 19,338,891 - 19,435,234

ENSG00000290983
Size : 74,844 bases


Location : 21,562,427 - 21,637,271

ENSG00000283809
Size : 41,494 bases


Location : 18,893,751 - 18,935,245

ENSG00000287146
Size : 36,932 bases


Location : 19,279,492 - 19,316,424

PI4KAP1
Size : 44,322 bases


Location : 20,383,513 - 20,427,835

ENSG00000290981
Size : 40,684 bases


Location : 20,970,517 - 21,011,201

COMT
Size : 28,604 bases

pLI : 0 LOEUF : 1.7 sHet : 0.007 pHaplo : 0.27 pTriplo : 0.48
Location : 19,928,894 - 19,957,498

NOVEL
Size : 24,129 bases


Location : 20,326,328 - 20,350,457

NOVEL
Size : 29,384 bases


Location : 20,632,023 - 20,661,407

KNOWN
Size : 24,500 bases


Location : 20,692,438 - 20,716,938

ENSG00000290950
Size : 22,118 bases


Location : 20,704,868 - 20,726,986

SMPD4P1
Size : 23,539 bases


Location : 20,956,882 - 20,980,421

ENSG00000291240
Size : 24,325 bases


Location : 21,362,536 - 21,386,861

FAM230B
Size : 24,398 bases


Location : 21,522,047 - 21,546,445

FAM230H
Size : 24,052 bases


Location : 21,655,279 - 21,679,331

ENSG00000284294
Size : 11,330 bases


Location : 18,923,924 - 18,935,254

ENSG00000280418
Size : 7,578 bases


Location : 18,939,447 - 18,947,025

CELSR1P1
Size : 8,665 bases


Location : 18,973,349 - 18,982,014

ENSG00000284874
Size : 7,552 bases


Location : 19,704,743 - 19,712,295

RTL10
Size : 8,758 bases


Location : 19,833,661 - 19,842,419

ENSG00000289960
Size : 12,447 bases


Location : 19,842,495 - 19,854,942

ENSG00000236540
Size : 12,539 bases


Location : 20,045,553 - 20,058,092

PRODHLP
Size : 13,456 bases


Location : 20,287,283 - 20,300,739

FAM247B
Size : 10,393 bases


Location : 20,351,661 - 20,362,054

PI4KAP1
Size : 14,793 bases


Location : 20,383,872 - 20,398,665

ENSG00000288811
Size : 11,078 bases


Location : 20,620,244 - 20,631,322

USP41
Size : 13,630 bases

pLI : 0 LOEUF : 1.21
Location : 20,717,911 - 20,731,541

ENSG00000277971
Size : 17,379 bases


Location : 20,783,528 - 20,800,907

POM121L4P
Size : 9,009 bases


Location : 21,044,217 - 21,053,226

LINC01637
Size : 7,590 bases


Location : 21,311,380 - 21,318,970

ENSG00000285314
Size : 18,659 bases


Location : 21,333,751 - 21,352,410

THAP7-AS1
Size : 8,456 bases


Location : 21,356,175 - 21,364,631

ENSG00000226872
Size : 12,763 bases


Location : 21,385,643 - 21,398,406

ENSG00000290799
Size : 9,769 bases


Location : 21,389,532 - 21,399,301

LRRC74B
Size : 18,222 bases

pLI : 0 LOEUF : 1.83
Location : 21,400,235 - 21,418,457

ENSG00000284665
Size : 9,936 bases


Location : 21,425,371 - 21,435,307

ENSG00000291044
Size : 19,302 bases


Location : 21,457,273 - 21,476,575

ENSG00000197210
Size : 9,844 bases


Location : 21,468,896 - 21,478,740

ENSG00000290961
Size : 10,395 bases


Location : 21,547,649 - 21,558,044

ENSG00000283583
Size : 630 bases


Location : 18,968,208 - 18,968,838

ENSG00000271275
Size : 457 bases


Location : 18,984,651 - 18,985,108

ENSG00000283366
Size : 153 bases


Location : 19,001,866 - 19,002,019

ENSG00000270393
Size : 873 bases


Location : 19,005,556 - 19,006,429

FAM246C
Size : 1,718 bases


Location : 19,017,037 - 19,018,755

CA15P1
Size : 3,000 bases


Location : 19,019,077 - 19,022,077

NOVEL
Size : 111 bases


Location : 19,032,769 - 19,032,880

DGCR11
Size : 2,213 bases


Location : 19,033,675 - 19,035,888

ENSG00000237347
Size : 711 bases


Location : 19,043,314 - 19,044,025

ENSG00000281530
Size : 802 bases


Location : 19,048,554 - 19,049,356

ENSG00000223461
Size : 2,974 bases


Location : 19,109,042 - 19,112,016

ENSG00000272682
Size : 4,140 bases


Location : 19,111,822 - 19,115,962

TSSK1A
Size : 767 bases


Location : 19,112,392 - 19,113,159

ENSG00000289481
Size : 798 bases


Location : 19,158,329 - 19,159,127

LINC01311
Size : 1,456 bases


Location : 19,158,908 - 19,160,364

ENSG00000286367
Size : 3,681 bases


Location : 19,183,913 - 19,187,594

ENSG00000230194
Size : 296 bases


Location : 19,225,966 - 19,226,262

NOVEL
Size : 93 bases


Location : 19,237,396 - 19,237,489

KRT18P62
Size : 1,286 bases


Location : 19,245,043 - 19,246,329

KNOWN
Size : 276 bases


Location : 19,353,289 - 19,353,565

UFD1-AS1
Size : 2,212 bases


Location : 19,435,416 - 19,437,628

ENSG00000273300
Size : 426 bases


Location : 19,441,702 - 19,442,128

ENSG00000273212
Size : 459 bases


Location : 19,444,026 - 19,444,485

ENSG00000287652
Size : 2,197 bases


Location : 19,508,095 - 19,510,292

LINC00895
Size : 1,636 bases


Location : 19,552,726 - 19,554,362

ENSG00000230485
Size : 2,824 bases


Location : 19,618,273 - 19,621,097

ENSG00000225007
Size : 532 bases


Location : 19,654,546 - 19,655,078

RPL7AP70
Size : 800 bases


Location : 19,779,817 - 19,780,617

ENSG00000232926
Size : 681 bases


Location : 19,874,812 - 19,875,493

ENSG00000289946
Size : 5,837 bases


Location : 19,921,184 - 19,927,021

KNOWN
Size : 81 bases


Location : 19,951,276 - 19,951,357

KNOWN
Size : 81 bases


Location : 20,020,662 - 20,020,743

ENSG00000268292
Size : 1,153 bases


Location : 20,052,075 - 20,053,228

KNOWN
Size : 87 bases


Location : 20,073,269 - 20,073,356

KNOWN
Size : 84 bases


Location : 20,073,581 - 20,073,665

ENSG00000243762
Size : 1,054 bases


Location : 20,098,344 - 20,099,398

NOVEL
Size : 124 bases


Location : 20,113,925 - 20,114,049

CCDC188
Size : 2,639 bases

pLI : 0 LOEUF : 1.16
Location : 20,135,939 - 20,138,578

LINC02891
Size : 6,189 bases


Location : 20,186,252 - 20,192,441

LINC00896
Size : 2,144 bases


Location : 20,193,903 - 20,196,047

KNOWN
Size : 77 bases


Location : 20,236,657 - 20,236,734

ENSG00000273343
Size : 630 bases


Location : 20,305,642 - 20,306,272

ENSG00000273139
Size : 1,104 bases


Location : 20,307,627 - 20,308,731

ENSG00000235578
Size : 1,162 bases


Location : 20,330,726 - 20,331,888

ENSG00000277017
Size : 4,248 bases


Location : 20,336,866 - 20,341,114

TMEM191B
Size : 2,771 bases


Location : 20,377,669 - 20,380,440

NOVEL
Size : 76 bases


Location : 20,434,077 - 20,434,153

NOVEL
Size : 142 bases


Location : 20,455,222 - 20,455,364

NOVEL
Size : 82 bases


Location : 20,455,450 - 20,455,532

KNOWN
Size : 300 bases


Location : 20,455,669 - 20,455,969

SUSD2P2
Size : 1,950 bases


Location : 20,473,206 - 20,475,156

FAM246B
Size : 698 bases


Location : 20,483,851 - 20,484,549

CA15P2
Size : 1,960 bases


Location : 20,486,312 - 20,488,272

PPP1R26P2
Size : 3,594 bases


Location : 20,499,890 - 20,503,484

GGTLC5P
Size : 5,754 bases


Location : 20,610,447 - 20,616,201

NOVEL
Size : 1,583 bases


Location : 20,644,408 - 20,645,991

PPP1R26P3
Size : 3,799 bases


Location : 20,670,709 - 20,674,508

ENSG00000287446
Size : 5,629 bases


Location : 20,703,048 - 20,708,677

KNOWN
Size : 102 bases


Location : 20,771,087 - 20,771,189

ENSG00000215493
Size : 1,702 bases


Location : 20,804,409 - 20,806,111

NOVEL
Size : 108 bases


Location : 20,829,490 - 20,829,598

NOVEL
Size : 110 bases


Location : 20,835,445 - 20,835,555

KNOWN
Size : 273 bases


Location : 20,836,224 - 20,836,497

KRT18P5
Size : 1,290 bases


Location : 20,837,102 - 20,838,392

NOVEL
Size : 91 bases


Location : 20,837,512 - 20,837,603

ENSG00000236003
Size : 1,800 bases


Location : 20,876,357 - 20,878,157

CCDC74BP1
Size : 4,722 bases


Location : 20,941,783 - 20,946,505

IGLL4P
Size : 132 bases


Location : 20,986,906 - 20,987,038

SLC9A3P2
Size : 2,020 bases


Location : 21,007,017 - 21,009,037

NOVEL
Size : 81 bases


Location : 21,011,322 - 21,011,403

ABHD17AP4
Size : 3,148 bases


Location : 21,022,124 - 21,025,272

ENSG00000290982
Size : 1,286 bases


Location : 21,044,319 - 21,045,605

BCRP5
Size : 972 bases


Location : 21,052,250 - 21,053,222

TMEM191A
Size : 3,492 bases


Location : 21,055,402 - 21,058,894

TMEM191A
Size : 2,483 bases


Location : 21,056,295 - 21,058,778

NOVEL
Size : 2,873 bases


Location : 21,077,335 - 21,080,208

ENSG00000272600
Size : 2,008 bases


Location : 21,243,494 - 21,245,502

KNOWN
Size : 265 bases


Location : 21,309,449 - 21,309,714

ENSG00000272829
Size : 882 bases


Location : 21,335,640 - 21,336,522

ENSG00000284060
Size : 6,558 bases


Location : 21,357,184 - 21,363,742

NOVEL
Size : 2,706 bases


Location : 21,358,030 - 21,360,736

TUBA3FP
Size : 6,099 bases


Location : 21,362,482 - 21,368,581

KNOWN
Size : 96 bases


Location : 21,388,465 - 21,388,561

P2RX6P
Size : 2,674 bases


Location : 21,396,632 - 21,399,306

TUBA3GP
Size : 4,635 bases


Location : 21,419,751 - 21,424,386

BCRP2
Size : 3,829 bases


Location : 21,470,218 - 21,474,047

POM121L7P
Size : 2,403 bases


Location : 21,479,949 - 21,482,352

E2F6P2
Size : 747 bases


Location : 21,495,913 - 21,496,660

ENSG00000234503
Size : 1,983 bases


Location : 21,532,181 - 21,534,164

FAM247A
Size : 177 bases


Location : 21,557,743 - 21,557,920

ENSG00000283145
Size : 378 bases


Location : 21,583,049 - 21,583,427

E2F6P3
Size : 742 bases


Location : 21,622,450 - 21,623,192

POM121L8P
Size : 1,280 bases


Location : 21,637,170 - 21,638,450

BCRP6
Size : 3,826 bases


Location : 21,645,049 - 21,648,875

ENSG00000237407
Size : 1,984 bases


Location : 21,667,209 - 21,669,193

PPP1R26P5
Size : 3,663 bases


Location : 21,695,884 - 21,699,547

LINC01651
Size : 3,504 bases


Location : 21,708,852 - 21,712,356

FAM246A
Size : 698 bases


Location : 21,714,890 - 21,715,588

ENSG00000226534
Size : 1,881 bases


Location : 21,724,353 - 21,726,234

KNOWN
Size : 300 bases


Location : 21,743,480 - 21,743,780

NOVEL
Size : 82 bases


Location : 21,743,917 - 21,743,999

NOVEL
Size : 142 bases


Location : 21,744,085 - 21,744,227

NOVEL
Size : 76 bases


Location : 21,765,339 - 21,765,415

176 ClinGen CNV overlap(s) (>= 70% only)

0 Benign CNV    0 Likely benign CNV    0 Uncertain CNV    4 Likely pathogenic CNV    172 Pathogenic CNV

#1 Pathogenic (22q11.21)
Location : 18,886,914 - 21,811,991 | Size : 2,925,077 bases

Score : 1

Mean Coverage : 100 %


#2 Pathogenic (nssv582145)
Location : 18,891,525 - 21,796,215 | Size : 2,904,690 bases

Score : 0

Mean Coverage : 100 %


#3 Pathogenic (22q11.21)
Location : 18,900,754 - 21,800,277 | Size : 2,899,523 bases

Score : 1
Phenotype : DiGeorge syndrome

Mean Coverage : 100 %


#4 Pathogenic (22q11.21)
Location : 18,916,827 - 21,800,797 | Size : 2,883,970 bases

Score : 1

Mean Coverage : 100 %


#5 Pathogenic (22q11.21)
Location : 18,916,841 - 21,798,907 | Size : 2,882,066 bases

Score : 0
Phenotype : DiGeorge syndrome

Mean Coverage : 100 %


#6 Pathogenic (22q11.21)
Location : 18,916,841 - 21,798,907 | Size : 2,882,066 bases

Score : 0

Mean Coverage : 100 %


#7 Pathogenic (nssv13649789)
Location : 18,916,841 - 21,804,716 | Size : 2,887,875 bases

Score : 0

Mean Coverage : 100 %


#8 Pathogenic (nssv3396760)
Location : 18,916,841 - 21,804,886 | Size : 2,888,045 bases

Score : 0

Mean Coverage : 100 %


#9 Pathogenic (22q11.21)
Location : 18,916,842 - 21,800,471 | Size : 2,883,629 bases

Score : 1

Mean Coverage : 100 %


#10 Pathogenic (22q11.21)
Location : 18,919,476 - 21,800,471 | Size : 2,880,995 bases

Score : 0
Phenotype : Velocardiofacial syndrome,DiGeorge syndrome

Mean Coverage : 100 %


#11 Pathogenic (22q11.21)
Location : 18,844,631 - 21,797,812 | Size : 2,953,181 bases

Score : 1

Mean Coverage : 99 %


#12 Pathogenic (nssv580005)
Location : 18,919,941 - 21,809,009 | Size : 2,889,068 bases

Score : 1

Mean Coverage : 99 %


#13 Pathogenic (22q11.21)
Location : 18,878,408 - 21,907,671 | Size : 3,029,263 bases

Score : 0

Mean Coverage : 98 %


#14 Pathogenic (22q11.21)
Location : 18,889,489 - 21,917,190 | Size : 3,027,701 bases

Score : 1

Mean Coverage : 98 %


#15 Pathogenic (22q11.21)
Location : 18,916,842 - 21,915,509 | Size : 2,998,667 bases

Score : 1

Mean Coverage : 98 %


#16 Pathogenic (nssv579989)
Location : 18,706,000 - 21,809,009 | Size : 3,103,009 bases

Score : 1

Mean Coverage : 97 %


#17 Pathogenic (22q11.21)
Location : 18,728,117 - 21,811,991 | Size : 3,083,874 bases

Score : 0

Mean Coverage : 97 %


#18 Pathogenic (22q11.21)
Location : 18,893,343 - 21,650,280 | Size : 2,756,937 bases

Score : 0
Phenotype : DiGeorge syndrome

Mean Coverage : 97 %


#19 Pathogenic (22q11.21)
Location : 18,626,107 - 21,800,797 | Size : 3,174,690 bases

Score : 0

Mean Coverage : 96 %


#20 Pathogenic (22q11.21)
Location : 18,631,363 - 21,800,471 | Size : 3,169,108 bases

Score : 0
Phenotype : Velocardiofacial syndrome,DiGeorge syndrome

Mean Coverage : 96 %


#21 Pathogenic (22q11.21)
Location : 18,636,748 - 21,800,471 | Size : 3,163,723 bases

Score : 0
Phenotype : Velocardiofacial syndrome,DiGeorge syndrome

Mean Coverage : 96 %


#22 Pathogenic (22q11.21)
Location : 18,644,542 - 21,800,797 | Size : 3,156,255 bases

Score : 1

Mean Coverage : 96 %


#23 Pathogenic (22q11.21)
Location : 18,644,789 - 21,800,471 | Size : 3,155,682 bases

Score : 0
Phenotype : DiGeorge syndrome

Mean Coverage : 96 %


#24 Pathogenic (22q11.21)
Location : 18,644,789 - 21,798,907 | Size : 3,154,118 bases

Score : 0
Phenotype : DiGeorge syndrome

Mean Coverage : 96 %


#25 Pathogenic (22q11.21)
Location : 18,645,352 - 21,800,797 | Size : 3,155,445 bases

Score : 0
Phenotype : DiGeorge syndrome

Mean Coverage : 96 %


#26 Pathogenic (22q11.21)
Location : 18,648,865 - 21,800,797 | Size : 3,151,932 bases

Score : 0

Mean Coverage : 96 %


#27 Pathogenic (22q11.21)
Location : 18,648,865 - 21,798,907 | Size : 3,150,042 bases

Score : 0
Phenotype : DiGeorge syndrome

Mean Coverage : 96 %


#28 Pathogenic (nssv582649)
Location : 18,661,723 - 21,809,009 | Size : 3,147,286 bases

Score : 0

Mean Coverage : 96 %


#29 Pathogenic (22q11.21)
Location : 18,844,631 - 21,608,479 | Size : 2,763,848 bases

Score : 0

Mean Coverage : 96 %


#30 Likely pathogenic (del)
Location : 18,861,208 - 21,630,630 | Size : 2,769,422 bases

Score : 1
Phenotype : Megacolon

Mean Coverage : 96 %


#31 Pathogenic (Single allele)
Location : 18,893,881 - 21,563,420 | Size : 2,669,539 bases

Score : 1
Phenotype : DiGeorge syndrome

Mean Coverage : 96 %


#32 Pathogenic (Single allele)
Location : 18,893,881 - 21,571,027 | Size : 2,677,146 bases

Score : 1
Phenotype : DiGeorge syndrome

Mean Coverage : 96 %


#33 Pathogenic (22q11.21)
Location : 18,893,887 - 21,570,386 | Size : 2,676,499 bases

Score : 1

Mean Coverage : 96 %


#34 Pathogenic (nssv575800)
Location : 18,894,834 - 21,561,514 | Size : 2,666,680 bases

Score : 0

Mean Coverage : 96 %


#35 Likely pathogenic (22q11.21)
Location : 18,655,797 - 21,726,191 | Size : 3,070,394 bases

Score : 0
Phenotype : Syndromic anorectal malformation

Mean Coverage : 95 %


#36 Pathogenic (22q11.21)
Location : 18,660,134 - 21,737,597 | Size : 3,077,463 bases

Score : 1
Phenotype : Chromosome 22q11.2 deletion syndrome,distal

Mean Coverage : 95 %


#37 Pathogenic (nssv582358)
Location : 18,765,084 - 21,661,435 | Size : 2,896,351 bases

Score : 0

Mean Coverage : 95 %


#38 Pathogenic (22q11.21)
Location : 18,765,101 - 21,661,435 | Size : 2,896,334 bases

Score : 0

Mean Coverage : 95 %


#39 Likely pathogenic (Single allele)
Location : 18,789,964 - 21,591,197 | Size : 2,801,233 bases

Score : 1
Phenotype : Inherited Immunodeficiency Diseases

Mean Coverage : 95 %


#40 Pathogenic (Single allele)
Location : 18,890,263 - 21,540,347 | Size : 2,650,084 bases

Score : 1
Phenotype : Neurodevelopmental disorder

Mean Coverage : 95 %


#41 Pathogenic (22q11.21)
Location : 18,894,834 - 21,505,417 | Size : 2,610,583 bases

Score : 1
Phenotype : 14 conditions

Mean Coverage : 95 %


#42 Pathogenic (nssv575807)
Location : 18,894,834 - 21,505,417 | Size : 2,610,583 bases

Score : 0

Mean Coverage : 95 %


#43 Pathogenic (nssv580035)
Location : 18,919,941 - 21,561,514 | Size : 2,641,573 bases

Score : 2

Mean Coverage : 95 %


#44 Pathogenic (nssv576777)
Location : 18,919,941 - 21,561,514 | Size : 2,641,573 bases

Score : 0

Mean Coverage : 95 %


#45 Pathogenic (22q11.21)
Location : 18,639,779 - 21,910,280 | Size : 3,270,501 bases

Score : 0
Phenotype : Syndromic anorectal malformation

Mean Coverage : 94 %


#46 Pathogenic (22q11.21)
Location : 18,644,789 - 21,915,509 | Size : 3,270,720 bases

Score : 0

Mean Coverage : 94 %


#47 Pathogenic (22q11.21)
Location : 18,872,507 - 21,465,050 | Size : 2,592,543 bases

Score : 0

Mean Coverage : 94 %


#48 Pathogenic (22q11.21)
Location : 18,875,868 - 21,470,273 | Size : 2,594,405 bases

Score : 0

Mean Coverage : 94 %


#49 Pathogenic (22q11.21)
Location : 18,875,955 - 21,466,715 | Size : 2,590,760 bases

Score : 0

Mean Coverage : 94 %


#50 Pathogenic (nssv1610455)
Location : 18,876,629 - 21,465,659 | Size : 2,589,030 bases

Score : 0

Mean Coverage : 94 %


#51 Pathogenic (22q11.21)
Location : 18,878,408 - 21,465,050 | Size : 2,586,642 bases

Score : 0

Mean Coverage : 94 %


#52 Pathogenic (22q11.21)
Location : 18,884,513 - 21,484,289 | Size : 2,599,776 bases

Score : 0

Mean Coverage : 94 %


#53 Pathogenic (22q11.21)
Location : 18,884,713 - 21,483,289 | Size : 2,598,576 bases

Score : 1

Mean Coverage : 94 %


#54 Pathogenic (22q11.21)
Location : 18,886,914 - 21,467,387 | Size : 2,580,473 bases

Score : 0

Mean Coverage : 94 %


#55 Pathogenic (22q11.21)
Location : 18,886,914 - 21,465,050 | Size : 2,578,136 bases

Score : 0

Mean Coverage : 94 %


#56 Pathogenic (Single allele)
Location : 18,886,914 - 21,463,730 | Size : 2,576,816 bases

Score : 0
Phenotype : Intellectual disability

Mean Coverage : 94 %


#57 Pathogenic (22q11.21)
Location : 18,886,914 - 21,463,730 | Size : 2,576,816 bases

Score : 1

Mean Coverage : 94 %


#58 Pathogenic (22q11.21)