CLCNKA : c.1600C>T

CLCNKA gene summary

Variant Details

Variant (CDS)Variant (protein)Variant Type Variant EffectGenomic Location (GRCh37)ExAC Frequency
c.1600C>Tp.R534W (Arg > Trp)substitutionmissense chr1:16357147 (forward strand)0.07875388

Effect in Cardiac Disease

As this variant is present at a population frequency of 0.07875388 (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
ExAC0.09775685
6415 / 65622		0.08967818
914 / 10192		0.00255339
22 / 8616		0.04354936
719 / 16510		0.03583825
413 / 11524		0.13374735
883 / 6602		0.09101124
81 / 890		0.07875388
9447 / 119956
ESP 0.09365
805 / 8596		 0.08583
378 / 4404
1183 / 13000
1KG
 0.07054
57 / 808		 0.08018
106 / 1322		 0.00595
6 / 1008		 0.04806
47 / 978		 0.04467
31 / 694		 0.10606
21 / 198		 0.05351
268 / 5008
View sub-population details for 1000 Genomes (1KG) data
Hide sub-population details for 1000 Genomes (1KG) data

0.05495
10 / 182
British
0.11475
14 / 122
African-American
0.00000
0 / 186
Chinese Dai
0.03488
6 / 172
Bengali
0.02128
4 / 188
Colombian
0.08411
18 / 214
Iberian
0.06250
12 / 192
African-Caribbean
0.00971
2 / 206
Han, Beijing
0.06311
13 / 206
Gujarati Indian
0.04688
6 / 128
Mexican, LA
0.04206
9 / 214
Toscani
0.05051
10 / 198
Esan, Nigeria
0.00962
2 / 208
Japanese
0.04902
10 / 204
Indian Telugu
0.01176
2 / 170
Peruvian
0.10101
20 / 198
Utah Europeans
0.07522
17 / 226
Gambian
0.01010
2 / 198
Kinh, Vietnam
0.03646
7 / 192
Punjabi, Lahore
0.09135
19 / 208
Puerto Rican
0.07071
14 / 198
Luhya, Kenya
0.00000
0 / 210
Southern Han
0.05392
11 / 204
Tamil
0.15294
26 / 170
Mende
0.06019
13 / 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
25% of algorithms have predicted that this variant will adversely affect protein function
tolerated moderately radical benign benign
LRT MutationTaster MutationAssessor FATHMM
neutral polymorphism 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.