COL11A1 : c.138T>G

COL11A1 gene summary

Variant Details

Variant (CDS)Variant (protein)Variant Type Variant EffectGenomic Location (GRCh37)ExAC Frequency
c.138T>Gp.D46E (Asp > Glu)substitutionmissense chr1:103548497 (reverse strand)0.06350542

Effect in Cardiac Disease

As this variant is present at a population frequency of 0.06350542 (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
ExAC0.07635076
5090 / 66666		0.12736944
1317 / 10340		0.00971323
84 / 8648		0.02290354
378 / 16504		0.03361636
388 / 11542		0.05943739
393 / 6612		0.05298013
48 / 906		0.06350542
7698 / 121218
ESP 0.08198
705 / 8600		 0.13164
580 / 4406		 0.09880
1285 / 13006
1KG
 0.08787
71 / 808		 0.12405
164 / 1322		 0.02083
21 / 1008		 0.01738
17 / 978		 0.04467
31 / 694		 0.06566
13 / 198		 0.06330
317 / 5008
View sub-population details for 1000 Genomes (1KG) data
Hide sub-population details for 1000 Genomes (1KG) data

0.10440
19 / 182
British
0.10656
13 / 122
African-American
0.01075
2 / 186
Chinese Dai
0.02326
4 / 172
Bengali
0.06915
13 / 188
Colombian
0.07477
16 / 214
Iberian
0.10938
21 / 192
African-Caribbean
0.03398
7 / 206
Han, Beijing
0.00000
0 / 206
Gujarati Indian
0.03125
4 / 128
Mexican, LA
0.07477
16 / 214
Toscani
0.14141
28 / 198
Esan, Nigeria
0.02404
5 / 208
Japanese
0.01471
3 / 204
Indian Telugu
0.01765
3 / 170
Peruvian
0.10101
20 / 198
Utah Europeans
0.20354
46 / 226
Gambian
0.02525
5 / 198
Kinh, Vietnam
0.03646
7 / 192
Punjabi, Lahore
0.05288
11 / 208
Puerto Rican
0.08586
17 / 198
Luhya, Kenya
0.00952
2 / 210
Southern Han
0.01471
3 / 204
Tamil
0.11765
20 / 170
Mende
0.08796
19 / 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

Missense Variant Predictions
SIFT Grantham Polyphen-DIV Polyphen-VAR Summary
12.5% of algorithms have predicted that this variant will adversely affect protein function
tolerated conservative benign benign
LRT MutationTaster MutationAssessor FATHMM
deleterious polymorphism (auto) neutral tolerated


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.