CASQ2 : c.196A>G

CASQ2 gene summary

Variant Details

Variant (CDS)Variant (protein)Variant Type Variant EffectGenomic Location (GRCh37)ExAC Frequency
c.196A>Gp.T66A (Thr > Ala)substitutionmissense chr1:116310967 (reverse strand)0.32650136

Effect in Cardiac Disease

As this variant is present at a population frequency of 0.32650136 (ExAC mean allelic frequency), it is highly unlikely to be pathogenic.

DCM

LMM:   Detected in 0 / 121 DCM patients.

For more information on the clinical significance of this variant, please see the ClinVar entry.

Detection in Population Databases



Database European African East Asian South Asian American Finnish Other Total
ExAC0.28372142
18935 / 66738		0.45377667
4722 / 10406		0.54828624
4735 / 8636		0.29990310
4952 / 16512		0.36351071
4208 / 11576		0.27305715
1806 / 6614		0.30396476
276 / 908		0.32650136
39634 / 121390
ESP 0.28907
2486 / 8600		 0.43759
1928 / 4406		 0.33938
4414 / 13006
1KG
 0.30941
250 / 808		 0.48563
642 / 1322		 0.51587
520 / 1008		 0.30470
298 / 978		 0.36744
255 / 694		 0.22222
44 / 198		 0.40116
2009 / 5008
View sub-population details for 1000 Genomes (1KG) data
Hide sub-population details for 1000 Genomes (1KG) data

0.29670
54 / 182
British
0.45082
55 / 122
African-American
0.55914
104 / 186
Chinese Dai
0.25581
44 / 172
Bengali
0.31915
60 / 188
Colombian
0.26168
56 / 214
Iberian
0.46354
89 / 192
African-Caribbean
0.49029
101 / 206
Han, Beijing
0.31068
64 / 206
Gujarati Indian
0.39062
50 / 128
Mexican, LA
0.36916
79 / 214
Toscani
0.44949
89 / 198
Esan, Nigeria
0.46635
97 / 208
Japanese
0.29412
60 / 204
Indian Telugu
0.37647
64 / 170
Peruvian
0.30808
61 / 198
Utah Europeans
0.46018
104 / 226
Gambian
0.50000
99 / 198
Kinh, Vietnam
0.36458
70 / 192
Punjabi, Lahore
0.38942
81 / 208
Puerto Rican
0.53535
106 / 198
Luhya, Kenya
0.56667
119 / 210
Southern Han
0.29412
60 / 204
Tamil
0.53529
91 / 170
Mende
0.50000
108 / 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 ENST00000261448 LRG_404t1NM_001232.3
Protein ENSP00000261448 LRG_404p1O14958

Missense Variant Predictions
SIFT Grantham Polyphen-DIV Polyphen-VAR Summary
0% of algorithms have predicted that this variant will adversely affect protein function
tolerated moderately conservative benign benign
LRT MutationTaster MutationAssessor FATHMM
neutral 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.