CLCNKA : c.1071T>A

CLCNKA gene summary

Variant Details

Variant (CDS)Variant (protein)Variant Type Variant EffectGenomic Location (GRCh37)ExAC Frequency
c.1071T>Ap.H357Q (His > Gln)substitutionmissense chr1:16355638 (forward strand)0.07668914

Effect in Cardiac Disease

As this variant is present at a population frequency of 0.07668914 (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
ExAC0.06476427
4176 / 64480		0.05130522
511 / 9960		0.09122725
782 / 8572		0.14138896
2325 / 16444		0.08781173
1000 / 11388		0.03217666
204 / 6340		0.06365741
55 / 864		0.07668914
9053 / 118048
ESP 0.06078
522 / 8588		 0.04607
203 / 4406		 0.05580
725 / 12994
1KG
 0.08168
66 / 808		 0.04387
58 / 1322		 0.09921
100 / 1008		 0.16155
158 / 978		 0.05620
39 / 694		 0.04545
9 / 198		 0.08586
430 / 5008
View sub-population details for 1000 Genomes (1KG) data
Hide sub-population details for 1000 Genomes (1KG) data

0.08791
16 / 182
British
0.07377
9 / 122
African-American
0.18280
34 / 186
Chinese Dai
0.18605
32 / 172
Bengali
0.05851
11 / 188
Colombian
0.04673
10 / 214
Iberian
0.05729
11 / 192
African-Caribbean
0.04854
10 / 206
Han, Beijing
0.14563
30 / 206
Gujarati Indian
0.07812
10 / 128
Mexican, LA
0.12617
27 / 214
Toscani
0.06061
12 / 198
Esan, Nigeria
0.04327
9 / 208
Japanese
0.13235
27 / 204
Indian Telugu
0.07059
12 / 170
Peruvian
0.06566
13 / 198
Utah Europeans
0.00442
1 / 226
Gambian
0.12121
24 / 198
Kinh, Vietnam
0.19792
38 / 192
Punjabi, Lahore
0.02885
6 / 208
Puerto Rican
0.08586
17 / 198
Luhya, Kenya
0.10952
23 / 210
Southern Han
0.15196
31 / 204
Tamil
0.01765
3 / 170
Mende
0.02315
5 / 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.