LDLR : c.1171G>A

LDLR gene summary

Variant Details

Variant (CDS)Variant (protein)Variant Type Variant EffectGenomic Location (GRCh37)ExAC Frequency
c.1171G>Ap.A391T (Ala > Thr)substitutionmissense chr19:11222300 (forward strand)0.04669945

Effect in Cardiac Disease

As this variant is present at a population frequency of 0.04669945 (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
ExAC0.04673281
3071 / 65714		0.18156042
1857 / 10228		0.00000000
0 / 8558		0.00514964
85 / 16506		0.02350390
271 / 11530		0.04307974
282 / 6546		0.04120267
37 / 898		0.04669945
5603 / 119980
ESP 0.04837
416 / 8600		 0.17295
762 / 4406		 0.09057
1178 / 13006
1KG
 0.04827
39 / 808		 0.20197
267 / 1322		 0.00000
0 / 1008		 0.00204
2 / 978		 0.03746
26 / 694		 0.02525
5 / 198		 0.06769
339 / 5008
View sub-population details for 1000 Genomes (1KG) data
Hide sub-population details for 1000 Genomes (1KG) data

0.05495
10 / 182
British
0.22131
27 / 122
African-American
0.00000
0 / 186
Chinese Dai
0.00000
0 / 172
Bengali
0.04787
9 / 188
Colombian
0.04673
10 / 214
Iberian
0.18750
36 / 192
African-Caribbean
0.00000
0 / 206
Han, Beijing
0.00485
1 / 206
Gujarati Indian
0.01562
2 / 128
Mexican, LA
0.03271
7 / 214
Toscani
0.16162
32 / 198
Esan, Nigeria
0.00000
0 / 208
Japanese
0.00000
0 / 204
Indian Telugu
0.00588
1 / 170
Peruvian
0.06061
12 / 198
Utah Europeans
0.19469
44 / 226
Gambian
0.00000
0 / 198
Kinh, Vietnam
0.00000
0 / 192
Punjabi, Lahore
0.06731
14 / 208
Puerto Rican
0.23232
46 / 198
Luhya, Kenya
0.00000
0 / 210
Southern Han
0.00490
1 / 204
Tamil
0.20588
35 / 170
Mende
0.21759
47 / 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 ENST00000558518 LRG_274t1NM_000527.4
Protein ENSP00000454071 LRG_274p1P01130

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 conservative benign benign
LRT MutationTaster MutationAssessor FATHMM
neutral polymorphism (auto) neutral damaging


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.