Length (hg19) : 3,800,000 bases - Length (hg38) : 3,087,403 bases
CNV-Hub AChro-Puce
Uncertain
AChro-Puce Criteria taken into account 1
2 Major
2 Minor
4 Major
4 Minor
4 Minor
ISV 2
XCNV 3
ClassifyCNV ACMG 4
AnnotSV ACMG 5
ACMG criteria
ClassifyCNV
2H
+
0.15
AnnotSV
2A
+
1
3C
+
0.9
ClinGen
0 benign CNV0 likely benign CNV
1 uncertain CNV
3 likely pathogenic CNV
12 pathogenic CNV
70% Overlaps
Decipher
0 benign CNV5 unknown CNV
4 uncertain CNV
4 pathogenic CNV
70% Overlaps
DGV-Gold
0
80% Overlaps
0
50% Overlaps
DGV
2
80% Overlaps
6
50% Overlaps
Coe & Al study 6
1
Patient cases
70% Overlaps
1
Controls
70% Overlaps
Genes in OMIM
12
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
0 Microdeletion and microduplication syndromes from litterature (>= 70% only)
12 OMIM Gene overlap(s)
Download genes as .csv
Location : 49,892,918 - 50,191,001
Database :
DecipherGenomics OMIM:613316 GTEx Portal Human Protein Atlas Ensembl
SFARI (Autism Database) :
Location : 49,654,079 - 49,864,310
Database :
DecipherGenomics OMIM:610585 GTEx Portal Human Protein Atlas Ensembl
Location : 49,514,682 - 49,647,403
Database :
DecipherGenomics PanelApp OMIM:601158 GTEx Portal Human Protein Atlas Ensembl
Location : 49,361,131 - 49,482,739
Database :
DecipherGenomics OMIM:613323 GTEx Portal Human Protein Atlas Ensembl
Location : 46,222,648 - 46,288,412
Database :
DecipherGenomics OMIM:613631 GTEx Portal Human Protein Atlas Ensembl
Location : 48,255,204 - 48,279,200
Database :
DecipherGenomics OMIM:602396 GTEx Portal Human Protein Atlas Ensembl
Location : 46,955,444 - 46,971,400
Database :
DecipherGenomics PanelApp OMIM:608081 GTEx Portal Human Protein Atlas Ensembl
Location : 46,992,959 - 47,007,881
Database :
DecipherGenomics OMIM:611240 GTEx Portal Human Protein Atlas Ensembl
Location : 48,425,785 - 48,439,165
Database :
DecipherGenomics OMIM:601361 GTEx Portal Human Protein Atlas Ensembl
Location : 48,381,481 - 48,390,999
Database :
DecipherGenomics PanelApp OMIM:180290 GTEx Portal Human Protein Atlas Ensembl
Location : 48,411,774 - 48,416,908
Database :
DecipherGenomics PanelApp OMIM:605120 GTEx Portal Human Protein Atlas Ensembl
Location : 47,083,457 - 47,088,320
Database :
DecipherGenomics OMIM:601790 GTEx Portal Human Protein Atlas Ensembl
104 Non-OMIM Gene overlap(s)
NOVEL
Size : 162,265 bases
Location : 47,011,753 - 47,174,018
ENSG00000289143
Size : 130,349 bases
Location : 49,218,162 - 49,348,511
KNOWN
Size : 91,090 bases
Location : 46,549,955 - 46,641,045
KNOWN
Size : 91,092 bases
Location : 48,736,874 - 48,827,966
ENSG00000289444
Size : 103,796 bases
Location : 49,244,696 - 49,348,492
ZFAND4
Size : 57,280 bases
Location : 46,110,948 - 46,168,228
KNOWN
Size : 62,078 bases
Location : 46,349,541 - 46,411,619
KNOWN
Size : 55,389 bases
Location : 47,894,023 - 47,949,412
KNOWN
Size : 53,415 bases
Location : 48,001,603 - 48,055,018
KNOWN
Size : 49,870 bases
Location : 48,901,102 - 48,950,972
PTPN20CP
Size : 55,150 bases
Location : 49,272,348 - 49,327,498
KNOWN
Size : 47,894 bases
Location : 47,191,844 - 47,239,738
NOVEL
Size : 35,697 bases
Location : 47,207,805 - 47,243,502
KNOWN
Size : 40,985 bases
Location : 47,379,727 - 47,420,712
ANTXRLP1
Size : 39,672 bases
Location : 47,605,121 - 47,644,793
ANTXRL
Size : 43,862 bases
Location : 47,657,581 - 47,701,443
FAM245B
Size : 30,723 bases
Location : 48,119,958 - 48,150,681
KNOWN
Size : 47,896 bases
Location : 48,189,612 - 48,237,508
LINC02675
Size : 30,813 bases
Location : 48,987,624 - 49,018,437
ENSG00000290899
Size : 34,945 bases
Location : 49,313,240 - 49,348,185
AGAP10P
Size : 21,840 bases
Location : 46,174,140 - 46,195,980
FAM21FP
Size : 16,008 bases
Location : 46,201,879 - 46,217,887
AGAP4
Size : 28,281 bases
Location : 46,321,042 - 46,349,323
KNOWN
Size : 24,468 bases
Location : 46,657,135 - 46,681,603
KNOWN
Size : 15,946 bases
Location : 46,717,127 - 46,733,073
KNOWN
Size : 23,593 bases
Location : 46,737,612 - 46,761,205
SHLD2P1
Size : 20,974 bases
Location : 46,918,169 - 46,939,143
ENSG00000229227
Size : 14,236 bases
Location : 46,937,463 - 46,951,699
SYT15-AS1
Size : 17,442 bases
Location : 46,951,467 - 46,968,909
SYT15B
Size : 18,889 bases
Location : 46,952,511 - 46,971,400
KNOWN
Size : 16,110 bases
Location : 47,157,983 - 47,174,093
KNOWN
Size : 13,576 bases
Location : 47,228,366 - 47,241,942
NOVEL
Size : 10,760 bases
Location : 47,279,073 - 47,289,833
AGAP14P
Size : 21,480 bases
Location : 47,708,453 - 47,729,933
ENSG00000279458
Size : 11,909 bases
Location : 47,741,976 - 47,753,885
KNOWN
Size : 16,105 bases
Location : 47,746,936 - 47,763,041
NOVEL
Size : 23,909 bases
Location : 47,746,962 - 47,770,871
KNOWN
Size : 11,840 bases
Location : 48,187,416 - 48,199,256
KNOWN
Size : 12,880 bases
Location : 48,249,334 - 48,262,214
NOVEL
Size : 23,920 bases
Location : 48,255,279 - 48,279,199
ZNF488
Size : 18,797 bases
Location : 48,355,069 - 48,373,866
ENSG00000289299
Size : 17,549 bases
Location : 48,514,368 - 48,531,917
KNOWN
Size : 24,468 bases
Location : 48,844,036 - 48,868,504
KNOWN
Size : 27,778 bases
Location : 48,952,491 - 48,980,269
AGAP12P
Size : 21,719 bases
Location : 49,217,898 - 49,239,617
AGAP12P
Size : 21,501 bases
Location : 49,218,157 - 49,239,658
BMS1P7
Size : 9,756 bases
Location : 49,258,304 - 49,268,060
ENSG00000290460
Size : 9,205 bases
Location : 46,213,474 - 46,222,679
ENSG00000228702
Size : 344 bases
Location : 46,221,142 - 46,221,486
ENSG00000270434
Size : 296 bases
Location : 46,308,096 - 46,308,392
FAM25E
Size : 1,896 bases
Location : 46,310,876 - 46,312,772
FAM25E
Size : 1,763 bases
Location : 46,310,934 - 46,312,697
RNA5SP310
Size : 115 bases
Location : 46,351,755 - 46,351,870
KNOWN
Size : 115 bases
Location : 46,742,028 - 46,742,143
KNOWN
Size : 6,100 bases
Location : 46,772,794 - 46,778,894
KNOWN
Size : 1,759 bases
Location : 46,773,447 - 46,775,206
KNOWN
Size : 1,118 bases
Location : 46,790,404 - 46,791,522
KNOWN
Size : 283 bases
Location : 46,900,386 - 46,900,669
LINC02637
Size : 3,085 bases
Location : 46,914,145 - 46,917,230
RHEBP1
Size : 555 bases
Location : 46,914,151 - 46,914,706
ENSG00000290913
Size : 9,216 bases
Location : 46,914,472 - 46,923,688
NPY4R2
Size : 4,863 bases
Location : 47,083,457 - 47,088,320
HNRNPA1P33
Size : 560 bases
Location : 47,133,338 - 47,133,898
ENSG00000273760
Size : 3,451 bases
Location : 47,135,135 - 47,138,586
KNOWN
Size : 297 bases
Location : 47,174,442 - 47,174,739
KNOWN
Size : 4,477 bases
Location : 47,177,204 - 47,181,681
NOVEL
Size : 5,982 bases
Location : 47,186,203 - 47,192,185
KNOWN
Size : 115 bases
Location : 47,222,341 - 47,222,456
KNOWN
Size : 1,760 bases
Location : 47,254,247 - 47,256,007
KNOWN
Size : 1,120 bases
Location : 47,271,222 - 47,272,342
KNOWN
Size : 283 bases
Location : 47,382,464 - 47,382,747
KNOWN
Size : 599 bases
Location : 47,396,223 - 47,396,822
KNOWN
Size : 3,359 bases
Location : 47,570,513 - 47,573,872
KNOWN
Size : 1,272 bases
Location : 47,594,379 - 47,595,651
KNOWN
Size : 1,149 bases
Location : 47,656,084 - 47,657,233
FAM25BP
Size : 4,437 bases
Location : 47,740,330 - 47,744,767
ENSG00000290780
Size : 3,260 bases
Location : 47,741,564 - 47,744,824
KNOWN
Size : 1,563 bases
Location : 47,965,760 - 47,967,323
CTSLP2
Size : 6,142 bases
Location : 48,152,549 - 48,158,691
KNOWN
Size : 1,107 bases
Location : 48,157,041 - 48,158,148
KNOWN
Size : 6,145 bases
Location : 48,169,665 - 48,175,810
KNOWN
Size : 1,759 bases
Location : 48,173,347 - 48,175,106
KNOWN
Size : 115 bases
Location : 48,206,895 - 48,207,010
KNOWN
Size : 4,474 bases
Location : 48,247,669 - 48,252,143
KNOWN
Size : 299 bases
Location : 48,254,606 - 48,254,905
KNOWN
Size : 7,409 bases
Location : 48,324,788 - 48,332,197
KNOWN
Size : 674 bases
Location : 48,357,926 - 48,358,600
NOVEL
Size : 98 bases
Location : 48,387,524 - 48,387,622
KNOWN
Size : 115 bases
Location : 48,931,789 - 48,931,904
ENSG00000265630
Size : 6,096 bases
Location : 48,962,529 - 48,968,625
KNOWN
Size : 946 bases
Location : 48,963,181 - 48,964,127
KNOWN
Size : 1,111 bases
Location : 48,980,162 - 48,981,273
KNOWN
Size : 7,117 bases
Location : 49,087,398 - 49,094,515
KNOWN
Size : 283 bases
Location : 49,090,136 - 49,090,419
FAM25C
Size : 4,470 bases
Location : 49,203,355 - 49,207,825
RNA5SP315
Size : 115 bases
Location : 49,248,476 - 49,248,591
NOVEL
Size : 809 bases
Location : 49,363,368 - 49,364,177
ENSG00000285786
Size : 1,987 bases
Location : 49,454,568 - 49,456,555
RPS6P14
Size : 718 bases
Location : 49,500,742 - 49,501,460
ENSG00000279822
Size : 1,984 bases
Location : 49,651,879 - 49,653,863
ARHGAP22-IT1
Size : 1,064 bases
Location : 49,718,568 - 49,719,632
ENSG00000231906
Size : 241 bases
Location : 49,754,517 - 49,754,758
ENSG00000251413
Size : 1,089 bases
Location : 49,832,049 - 49,833,138
ENSG00000236800
Size : 8,225 bases
Location : 49,872,244 - 49,880,469
17 ClinGen CNV overlap(s) (>= 70% only)
0 Benign CNV 0 Likely benign CNV 1 Uncertain CNV 3 Likely pathogenic CNV 12 Pathogenic CNV
#1 Pathogenic (nssv583185)
Location : 46,205,689 - 51,330,432 |
Size : 5,124,743 bases
Score : 0
#2 Pathogenic (10q11.22-11.23)
Location : 46,491,168 - 51,081,560 |
Size : 4,590,392 bases
Score : 1
#3 Pathogenic (nssv13646749)
Location : 46,224,445 - 51,594,991 |
Size : 5,370,546 bases
Score : 0
#4 Pathogenic (nssv706778)
Location : 46,205,695 - 51,724,915 |
Size : 5,519,220 bases
Score : 0
#5 Pathogenic (10q11.22-11.23)
Location : 46,287,820 - 51,627,470 |
Size : 5,339,650 bases
Score : 0
#6 not provided (10q11.22-11.23)
Location : 46,321,317 - 51,595,050 |
Size : 5,273,733 bases
Score : 0
#7 Pathogenic (nssv579668)
Location : 46,205,689 - 51,911,085 |
Size : 5,705,396 bases
Score : 1
#8 Pathogenic (10q11.22-11.23)
Location : 46,225,363 - 51,874,356 |
Size : 5,648,993 bases
Score : 0
#9 Pathogenic (10q11.22-11.23)
Location : 46,235,356 - 51,874,163 |
Size : 5,638,807 bases
Score : 0
#10 Likely pathogenic (10q11.22-11.23)
Location : 46,269,492 - 51,874,356 |
Size : 5,604,864 bases
Score : 1
#11 Pathogenic (10q11.22-11.23)
Location : 46,287,820 - 51,861,565 |
Size : 5,573,745 bases
Score : 0
#12 Pathogenic (nssv583520)
Location : 46,491,168 - 51,594,991 |
Size : 5,103,823 bases
Score : 0
#13 Uncertain significance (nssv1610028)
Location : 46,476,964 - 51,724,915 |
Size : 5,247,951 bases
Score : 0
#14 Likely pathogenic (nssv1495736)
Location : 46,476,964 - 51,724,915 |
Size : 5,247,951 bases
Score : 0
#15 Likely pathogenic (nssv1602988)
Location : 46,491,168 - 51,664,079 |
Size : 5,172,911 bases
Score : 0
#16 Pathogenic (10q11.22-11.23)
Location : 46,544,809 - 51,743,471 |
Size : 5,198,662 bases
Score : 1
#17 Pathogenic (10q11.22-11.23)
Location : 46,576,514 - 51,680,164 |
Size : 5,103,650 bases
Score : 0
Phenotype :
Telangiectasia,hereditary hemorrhagic,type 5
13 Decipher CNV overlap(s) (>= 70% only)
0 Benign CNV 5 Unknown CNV 4 Uncertain CNV 4 Pathogenic CNV
#1 : unknown
Location : 46,248,489 - 51,572,974
| Size : 5,324,485 bases
Patient Id : 254072
Gender : Inconnu
Phenotype :
Glossoptosis, Cleft palate, Epicanthus, Hypertelorism, Micrognathia
#2 : uncertain
Location : 46,205,719 - 51,911,060
| Size : 5,705,341 bases
Patient Id : 339993
Gender : Inconnu
Phenotype :
Strabismus, Seizure, Mild global developmental delay
#3 : pathogenic
Location : 46,241,892 - 51,829,561
| Size : 5,587,669 bases
Patient Id : 295571
Gender : Inconnu
Phenotype :
Otitis media, Joint hypermobility, Short stature, Attention deficit hyperactivity disorder, Moderate global developmental delay
#4 : pathogenic
Location : 46,241,892 - 51,829,561
| Size : 5,587,669 bases
Patient Id : 295573
Gender : Inconnu
Phenotype :
Moderate global developmental delay
#5 : uncertain
Location : 46,264,301 - 51,780,909
| Size : 5,516,608 bases
Patient Id : 410947
Gender : Inconnu
Phenotype :
Autistic behavior, Loss of speech
#6 : pathogenic
Location : 46,241,892 - 52,000,417
| Size : 5,758,525 bases
Patient Id : 295572
Gender : Inconnu
Phenotype :
Joint hypermobility, Short stature, Dyslexia, Moderate global developmental delay
#7 : unknown
Location : 46,283,685 - 51,822,906
| Size : 5,539,221 bases
Patient Id : 259254
Gender : Inconnu
Phenotype :
Low\-set ears, Blepharophimosis, Pectus carinatum, Gynecomastia, Single transverse palmar crease, Hypotonia, Short stature
#8 : pathogenic
Location : 46,287,820 - 51,861,466
| Size : 5,573,646 bases
Patient Id : 327088
Gender : Inconnu
Phenotype :
Protruding ear, Congenital nystagmus, Uplifted earlobe, Unilateral microphthalmos, Anteverted ears
#9 : unknown
Location : 46,287,820 - 51,874,356
| Size : 5,586,536 bases
Patient Id : 263485
Gender : Inconnu
#10 : unknown
Location : 46,405,261 - 51,780,901
| Size : 5,375,640 bases
Patient Id : 260106
Gender : Inconnu
Phenotype :
Impaired social interactions, Specific learning disability, Cognitive impairment
#11 : unknown
Location : 46,342,336 - 52,020,271
| Size : 5,677,935 bases
Patient Id : 273399
Gender : Inconnu
Phenotype :
High palate, Short philtrum, Low\-set ears, Abnormality of the pinna, Strabismus, Myopia, Soft skin, Seizure, Intellectual disability, moderate, Inverted nipples, Posterior plagiocephaly, Anteverted ears
#12 : uncertain
Location : 46,215,429 - 52,467,181
| Size : 6,251,752 bases
Patient Id : 402953
Gender : Inconnu
#13 : uncertain
Location : 46,215,429 - 52,467,181
| Size : 6,251,752 bases
Patient Id : 404263
Gender : Inconnu
1 Gene(s) in SFARI Database
1 DGV-Gold overlap(s) (>= 50% only)
DGV-Gold #1
Location : 46,719,449 - 49,176,867
| Size : 2,457,418 bases
Frequency in Population : 3.17 %
Inner Rank : 9
6 DGV overlap(s) (>= 50% only)
DGV #1
Location : 46,021,713 - 48,481,919
| Size : 2,460,206 bases
DGV #2
Location : 46,045,761 - 47,593,951
| Size : 1,548,190 bases
DGV #3
Location : 46,109,533 - 48,312,291
| Size : 2,202,758 bases
DGV #4
Location : 46,677,594 - 49,272,522
| Size : 2,594,928 bases
DGV #5
Location : 46,680,255 - 49,378,479
| Size : 2,698,224 bases
DGV #6
Location : 46,802,558 - 48,992,343
| Size : 2,189,785 bases
1 Patient cases (>= 70% only)
47,006,953 - 51,330,432
Size : 4,323,479 bases
7 Reports
1 Controls (>= 70% only)
nssv3707830
Location : 46527664 - 51911841 | Size : 5384177 bases
4 Gene(s) in PanelApp Database
| Confidence | Disease | Inheritance | Phenotype | Evidence |
|---|---|---|---|---|
| Low | Primary immunodeficiency or monogenic inflammatory bowel disease | MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown |
- chronic mucocutaneous candidiasis - connective tissue disorders |
- Expert Review Red - Literature |
| Confidence | Disease | Inheritance | Phenotype | Evidence |
|---|---|---|---|---|
| Low | Glaucoma (developmental) |
- Eye Disorders |
- NHS GMS - Emory Genetics Laboratory |
|
| High | Retinal disorders | BIALLELIC, autosomal or pseudoautosomal |
- Eye Disorders - Retinitis Pigmentosa, Recessive - Retinitis pigmentosa - ?Retinitis pigmentosa 66, 615233 |
- NHS GMS - Expert Review Green |
| Low | Structural eye disease | BIALLELIC, autosomal or pseudoautosomal |
- ?Retinitis pigmentosa 66, 615233 - Eye Disorders |
- NHS GMS - Expert Review Red |
| Confidence | Disease | Inheritance | Phenotype | Evidence |
|---|---|---|---|---|
| Medium | Cerebral vascular malformations | MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted |
- Telangiectasia, hereditary hemorrhagic, type 5, OMIM:615506 |
- Yorkshire and North East GLH - NHS GMS - Expert Review Amber - Radboud University Medical Center, Nijmegen - UKGTN - Emory Genetics Laboratory |
| High | Hereditary haemorrhagic telangiectasia | MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted |
- Telangiectasia, hereditary hemorrhagic, type 5 OMIM:615506 - telangiectasia, hereditary hemorrhagic, type 5 MONDO:0014217 |
- Expert Review Green - NHS GMS - Expert Review - Radboud University Medical Center, Nijmegen - UKGTN - Emory Genetics Laboratory |
| High | Pulmonary arterial hypertension | MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown |
- Heritable pulmonary arterial hypertension - HPAH |
- NHS GMS - Expert Review Green - Literature |
| Low | Fetal anomalies | BIALLELIC, autosomal or pseudoautosomal |
- Lymphatic dysplasia - hydrothorax - hydrops |
- Expert Review Red - Literature |