COL11A1 : c.1998+4T>A

COL11A1 gene summary

Variant Details

Variant (CDS)Variant (protein)Variant Type Variant EffectGenomic Location (GRCh37)ExAC Frequency
c.1998+4T>Asubstitutionsplice site chr1:103468767 (reverse strand)0.12289806

Effect in Cardiac Disease

As this variant is present at a population frequency of 0.12289806 (ExAC mean allelic frequency), it is highly unlikely to be pathogenic.

Detection in Population Databases



Database European African East Asian South Asian American Finnish Other Total
ExAC0.14516079
9335 / 64308		0.05142255
488 / 9490		0.00143850
12 / 8342		0.07035872
1118 / 15890		0.19783447
2156 / 10898		0.16272189
1045 / 6422		0.14906103
127 / 852		0.12289806
14281 / 116202
ESP 0.13384
1151 / 8600		 0.05175
228 / 4406		 0.10603
1379 / 13006
1KG
 0.11757
95 / 808		 0.04085
54 / 1322		 0.00000
0 / 1008		 0.06033
59 / 978		 0.17435
121 / 694		 0.17677
35 / 198		 0.07268
364 / 5008
View sub-population details for 1000 Genomes (1KG) data
Hide sub-population details for 1000 Genomes (1KG) data

0.11538
21 / 182
British
0.05738
7 / 122
African-American
0.00000
0 / 186
Chinese Dai
0.07558
13 / 172
Bengali
0.17021
32 / 188
Colombian
0.11682
25 / 214
Iberian
0.04688
9 / 192
African-Caribbean
0.00000
0 / 206
Han, Beijing
0.05825
12 / 206
Gujarati Indian
0.19531
25 / 128
Mexican, LA
0.12150
26 / 214
Toscani
0.03535
7 / 198
Esan, Nigeria
0.00000
0 / 208
Japanese
0.07353
15 / 204
Indian Telugu
0.29412
50 / 170
Peruvian
0.11616
23 / 198
Utah Europeans
0.04867
11 / 226
Gambian
0.00000
0 / 198
Kinh, Vietnam
0.04688
9 / 192
Punjabi, Lahore
0.06731
14 / 208
Puerto Rican
0.04040
8 / 198
Luhya, Kenya
0.00000
0 / 210
Southern Han
0.04902
10 / 204
Tamil
0.05294
9 / 170
Mende
0.01389
3 / 216
Yoruba, Nigeria

The Exome Aggregation Consortium (ExAC) is a database of 60,706 unrelated individuals sequenced as part of various disease-specific and population genetic studies. There is partial overlap between ExAC and 1000 Genomes (1KG) (1,851 of the 2,504 samples in 1KG) and the Exome Sequencing Project (ESP) (3,936 of the 6,500 samples in ESP).


Other Variant & Gene Details

Canonical Sequences
Transcript ENST00000370096 NM_001854.3
Protein ENSP00000359114 P12107



References

1. Roddy Walsh, Kate L. Thomson, James S. Ware, Birgit H. Funke, Jessica Woodley, Karen J. McGuire, Francesco Mazzarotto, Edward Blair, Anneke Seller, Jenny C. Taylor, Eric V. Minikel, Exome Aggregation Consortium, Daniel G. MacArthur, Martin Farrall, Stuart A. Cook and Hugh Watkins. Reassessment of Mendelian gene pathogenicity using 7,855 cardiomyopathy cases and 60,706 reference samples. Genet Med. 2016 doi:10.1038/gim.2016.90.

2. Pugh TJ, Kelly MA, Gowrisankar S, Hynes E, Seidman MA, Baxter SM, Bowser M, Harrison B, Aaron D, Mahanta LM, Lakdawala NK, McDermott G, White ET, Rehm HL, Lebo M, Funke BH. The landscape of genetic variation in dilated cardiomyopathy as surveyed by clinical DNA sequencing. Genet Med. 2014 Aug;16(8):601-8.

3. Alfares AA, Kelly MA, McDermott G, Funke BH, Lebo MS, Baxter SB, Shen J, McLaughlin HM, Clark EH, Babb LJ, Cox SW, DePalma SR, Ho CY, Seidman JG, Seidman CE, Rehm HL. Results of clinical genetic testing of 2,912 probands with hypertrophic cardiomyopathy: expanded panels offer limited additional sensitivity. Genet Med. 2015 Nov;17(11):880-8.