CASQ2 : c.420+6T>C

CASQ2 gene summary

Variant Details

Variant (CDS)Variant (protein)Variant Type Variant EffectGenomic Location (GRCh37)ExAC Frequency
c.420+6T>Csubstitutionsplice site chr1:116283343 (reverse strand)0.78716546

Effect in Cardiac Disease

As this variant is present at a population frequency of 0.78716546 (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
ExAC0.86893889
57847 / 66572		0.36018590
3720 / 10328		0.76267227
6530 / 8562		0.74031573
12193 / 16470		0.76519481
8838 / 11550		0.81600485
5384 / 6598		0.79911700
724 / 906		0.78716546
95236 / 120986
ESP 0.87802
7551 / 8600		 0.37744
1663 / 4406		 0.70844
9214 / 13006
1KG
 0.88366
714 / 808		 0.28139
372 / 1322		 0.74306
749 / 1008		 0.71063
695 / 978		 0.76081
528 / 694		 0.83333
165 / 198		 0.64357
3223 / 5008
View sub-population details for 1000 Genomes (1KG) data
Hide sub-population details for 1000 Genomes (1KG) data

0.89011
162 / 182
British
0.36885
45 / 122
African-American
0.86022
160 / 186
Chinese Dai
0.70930
122 / 172
Bengali
0.82979
156 / 188
Colombian
0.89720
192 / 214
Iberian
0.33333
64 / 192
African-Caribbean
0.72816
150 / 206
Han, Beijing
0.70388
145 / 206
Gujarati Indian
0.74219
95 / 128
Mexican, LA
0.87850
188 / 214
Toscani
0.28283
56 / 198
Esan, Nigeria
0.54808
114 / 208
Japanese
0.70098
143 / 204
Indian Telugu
0.68824
117 / 170
Peruvian
0.86869
172 / 198
Utah Europeans
0.24336
55 / 226
Gambian
0.79293
157 / 198
Kinh, Vietnam
0.80208
154 / 192
Punjabi, Lahore
0.76923
160 / 208
Puerto Rican
0.20707
41 / 198
Luhya, Kenya
0.80000
168 / 210
Southern Han
0.64216
131 / 204
Tamil
0.34118
58 / 170
Mende
0.24537
53 / 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



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.