LAMA2 : c.3412G>A

LAMA2 gene summary

Variant Details

Variant (CDS)Variant (protein)Variant Type Variant EffectGenomic Location (GRCh37)ExAC Frequency
c.3412G>Ap.V1138M (Val > Met)substitutionmissense chr6:129635800 (forward strand)0.06873277

Effect in Cardiac Disease

As this variant is present at a population frequency of 0.06873277 (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
ExAC0.04153379
2735 / 65850		0.19370341
1975 / 10196		0.14858271
1279 / 8608		0.08683041
1407 / 16204		0.05004390
570 / 11390		0.03077392
202 / 6564		0.06681514
60 / 898		0.06873277
8228 / 119710
ESP 0.04686
403 / 8600		 0.17749
782 / 4406		 0.09111
1185 / 13006
1KG
 0.04950
40 / 808		 0.21861
289 / 1322		 0.11111
112 / 1008		 0.12065
118 / 978		 0.05620
39 / 694		 0.01515
3 / 198		 0.12001
601 / 5008
View sub-population details for 1000 Genomes (1KG) data
Hide sub-population details for 1000 Genomes (1KG) data

0.08242
15 / 182
British
0.13934
17 / 122
African-American
0.05914
11 / 186
Chinese Dai
0.13953
24 / 172
Bengali
0.04255
8 / 188
Colombian
0.04673
10 / 214
Iberian
0.15625
30 / 192
African-Caribbean
0.11165
23 / 206
Han, Beijing
0.13107
27 / 206
Gujarati Indian
0.09375
12 / 128
Mexican, LA
0.03271
7 / 214
Toscani
0.22727
45 / 198
Esan, Nigeria
0.14423
30 / 208
Japanese
0.12745
26 / 204
Indian Telugu
0.02941
5 / 170
Peruvian
0.04040
8 / 198
Utah Europeans
0.35841
81 / 226
Gambian
0.07576
15 / 198
Kinh, Vietnam
0.08854
17 / 192
Punjabi, Lahore
0.06731
14 / 208
Puerto Rican
0.23737
47 / 198
Luhya, Kenya
0.15714
33 / 210
Southern Han
0.11765
24 / 204
Tamil
0.18824
32 / 170
Mende
0.17130
37 / 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
0% of algorithms have predicted that this variant will adversely affect protein function
conservative benign benign
LRT MutationTaster MutationAssessor FATHMM
neutral polymorphism (auto) low impact 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.