CALR3 : c.820G>A

CALR3 gene summary

Variant Details

Variant (CDS)Variant (protein)Variant Type Variant EffectGenomic Location (GRCh37)ExAC Frequency
c.820G>Ap.V274I (Val > Ile)substitutionmissense chr19:16593359 (reverse strand)0.03012058

Effect in Cardiac Disease

As this variant is present at a population frequency of 0.03012058 (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
ExAC0.00480971
321 / 66740		0.05150874
536 / 10406		0.02287959
198 / 8654		0.00520833
86 / 16512		0.21445846
2483 / 11578		0.00302389
20 / 6614		0.01431718
13 / 908		0.03012058
3657 / 121412
ESP 0.00593
51 / 8600		 0.04970
219 / 4406		 0.02076
270 / 13006
1KG
 0.00495
4 / 808		 0.05446
72 / 1322		 0.03075
31 / 1008		 0.00818
8 / 978		 0.13401
93 / 694		 0.01515
3 / 198		 0.04213
211 / 5008
View sub-population details for 1000 Genomes (1KG) data
Hide sub-population details for 1000 Genomes (1KG) data

0.00000
0 / 182
British
0.05738
7 / 122
African-American
0.02151
4 / 186
Chinese Dai
0.01163
2 / 172
Bengali
0.03191
6 / 188
Colombian
0.00935
2 / 214
Iberian
0.04688
9 / 192
African-Caribbean
0.05340
11 / 206
Han, Beijing
0.00000
0 / 206
Gujarati Indian
0.21875
28 / 128
Mexican, LA
0.00000
0 / 214
Toscani
0.03030
6 / 198
Esan, Nigeria
0.00962
2 / 208
Japanese
0.00000
0 / 204
Indian Telugu
0.29412
50 / 170
Peruvian
0.01010
2 / 198
Utah Europeans
0.04425
10 / 226
Gambian
0.03030
6 / 198
Kinh, Vietnam
0.01562
3 / 192
Punjabi, Lahore
0.04327
9 / 208
Puerto Rican
0.09091
18 / 198
Luhya, Kenya
0.03810
8 / 210
Southern Han
0.01471
3 / 204
Tamil
0.05882
10 / 170
Mende
0.05556
12 / 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 ENST00000269881 LRG_422t1NM_145046.3
Protein ENSP00000269881 LRG_422p1Q96L12

Missense Variant Predictions
SIFT Grantham Polyphen-DIV Polyphen-VAR Summary
0% of algorithms have predicted that this variant will adversely affect protein function
tolerated 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.