CLCNKA : c.944A>T

CLCNKA gene summary

Variant Details

Variant (CDS)Variant (protein)Variant Type Variant EffectGenomic Location (GRCh37)ExAC Frequency
c.944A>Tp.Y315F (Tyr > Phe)substitutionmissense chr1:16354590 (forward strand)0.20701425

Effect in Cardiac Disease

As this variant is present at a population frequency of 0.20701425 (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
ExAC0.21707507
14475 / 66682		0.13344237
1387 / 10394		0.22782025
1967 / 8634		0.11624667
1919 / 16508		0.25544606
2955 / 11568		0.33192005
2192 / 6604		0.23730684
215 / 906		0.20701425
25110 / 121296
ESP 0.21570
1855 / 8600		 0.13329
587 / 4404		 0.18779
2442 / 13004
1KG
 0.15842
128 / 808		 0.10136
134 / 1322		 0.21230
214 / 1008		 0.10327
101 / 978		 0.19597
136 / 694		 0.30808
61 / 198		 0.15455
774 / 5008
View sub-population details for 1000 Genomes (1KG) data
Hide sub-population details for 1000 Genomes (1KG) data

0.12637
23 / 182
British
0.16393
20 / 122
African-American
0.18817
35 / 186
Chinese Dai
0.11047
19 / 172
Bengali
0.23936
45 / 188
Colombian
0.18692
40 / 214
Iberian
0.09896
19 / 192
African-Caribbean
0.24272
50 / 206
Han, Beijing
0.10194
21 / 206
Gujarati Indian
0.20312
26 / 128
Mexican, LA
0.12150
26 / 214
Toscani
0.05051
10 / 198
Esan, Nigeria
0.25000
52 / 208
Japanese
0.10294
21 / 204
Indian Telugu
0.18824
32 / 170
Peruvian
0.19697
39 / 198
Utah Europeans
0.09292
21 / 226
Gambian
0.19192
38 / 198
Kinh, Vietnam
0.08333
16 / 192
Punjabi, Lahore
0.15865
33 / 208
Puerto Rican
0.11111
22 / 198
Luhya, Kenya
0.18571
39 / 210
Southern Han
0.11765
24 / 204
Tamil
0.15882
27 / 170
Mende
0.06944
15 / 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 ENST00000331433 NM_004070.3
Protein ENSP00000332771 P51800

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
neutral polymorphism (auto) neutral damaging


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.