CALR3 : c.397+10C>T

CALR3 gene summary

Variant Details

Variant (CDS)Variant (protein)Variant Type Variant EffectGenomic Location (GRCh37)ExAC Frequency
c.397+10C>Tsubstitutionsplice site chr19:16601168 (reverse strand)0.12205555

Effect in Cardiac Disease

As this variant is present at a population frequency of 0.12205555 (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
ExAC0.13615917
9081 / 66694		0.10792613
1122 / 10396		0.09470398
819 / 8648		0.11224861
1853 / 16508		0.06883431
796 / 11564		0.15744102
1041 / 6612		0.10682819
97 / 908		0.12205555
14809 / 121330
ESP 0.00000
0 / 8600		 0.00000
0 / 4400		 0.00000
0 / 13000
1KG
 0.13861
112 / 808		 0.10363
137 / 1322		 0.10417
105 / 1008		 0.12986
127 / 978		 0.09366
65 / 694		 0.12626
25 / 198		 0.11402
571 / 5008
View sub-population details for 1000 Genomes (1KG) data
Hide sub-population details for 1000 Genomes (1KG) data

0.12088
22 / 182
British
0.19672
24 / 122
African-American
0.12903
24 / 186
Chinese Dai
0.16279
28 / 172
Bengali
0.08511
16 / 188
Colombian
0.14953
32 / 214
Iberian
0.07292
14 / 192
African-Caribbean
0.07767
16 / 206
Han, Beijing
0.10680
22 / 206
Gujarati Indian
0.08594
11 / 128
Mexican, LA
0.13551
29 / 214
Toscani
0.05051
10 / 198
Esan, Nigeria
0.07692
16 / 208
Japanese
0.12255
25 / 204
Indian Telugu
0.04706
8 / 170
Peruvian
0.14646
29 / 198
Utah Europeans
0.12832
29 / 226
Gambian
0.14141
28 / 198
Kinh, Vietnam
0.08854
17 / 192
Punjabi, Lahore
0.14423
30 / 208
Puerto Rican
0.16162
32 / 198
Luhya, Kenya
0.10000
21 / 210
Southern Han
0.17157
35 / 204
Tamil
0.10000
17 / 170
Mende
0.05093
11 / 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



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.