LAMA2 : c.2756G>T

LAMA2 gene summary

Variant Details

Variant (CDS)Variant (protein)Variant Type Variant EffectGenomic Location (GRCh37)ExAC Frequency
c.2756G>Tp.R919L (Arg > Leu)substitutionmissense chr6:129612765 (forward strand)0.01430631

Effect in Cardiac Disease

As this variant is present at a population frequency of 0.01430631 (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
ExAC0.00089972
59 / 65576		0.14197892
1455 / 10248		0.00000000
0 / 8554		0.00681537
110 / 16140		0.00687588
78 / 11344		0.00000000
0 / 6562		0.00559284
5 / 894		0.01430631
1707 / 119318
ESP 0.00105
9 / 8600		 0.13323
587 / 4406		 0.04582
596 / 13006
1KG
 0.00248
2 / 808		 0.15734
208 / 1322		 0.00000
0 / 1008		 0.01227
12 / 978		 0.01441
10 / 694		 0.00000
0 / 198		 0.04633
232 / 5008
View sub-population details for 1000 Genomes (1KG) data
Hide sub-population details for 1000 Genomes (1KG) data

0.00549
1 / 182
British
0.13115
16 / 122
African-American
0.00000
0 / 186
Chinese Dai
0.00581
1 / 172
Bengali
0.01064
2 / 188
Colombian
0.00000
0 / 214
Iberian
0.11458
22 / 192
African-Caribbean
0.00000
0 / 206
Han, Beijing
0.01942
4 / 206
Gujarati Indian
0.03906
5 / 128
Mexican, LA
0.00467
1 / 214
Toscani
0.16162
32 / 198
Esan, Nigeria
0.00000
0 / 208
Japanese
0.01471
3 / 204
Indian Telugu
0.00588
1 / 170
Peruvian
0.00000
0 / 198
Utah Europeans
0.21239
48 / 226
Gambian
0.00000
0 / 198
Kinh, Vietnam
0.01042
2 / 192
Punjabi, Lahore
0.00962
2 / 208
Puerto Rican
0.15152
30 / 198
Luhya, Kenya
0.00000
0 / 210
Southern Han
0.00980
2 / 204
Tamil
0.16471
28 / 170
Mende
0.14815
32 / 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 ENST00000421865 LRG_409t1NM_000426.3
Protein ENSP00000400365 LRG_409p1P24043

Missense Variant Predictions
SIFT Grantham Polyphen-DIV Polyphen-VAR Summary
12.5% of algorithms have predicted that this variant will adversely affect protein function
tolerated moderately radical benign benign
LRT MutationTaster MutationAssessor FATHMM
neutral polymorphism 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.