SLCO1B1 : c.1929A>C

SLCO1B1 gene summary

Variant Details

Variant (CDS)Variant (protein)Variant Type Variant EffectGenomic Location (GRCh37)ExAC Frequency
c.1929A>Cp.L643F (Leu > Phe)substitutionmissense chr12:21391976 (forward strand)0.04632220

Effect in Cardiac Disease

As this variant is present at a population frequency of 0.04632220 (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
ExAC0.05177888
3327 / 64254		0.07123259
675 / 9476		0.00095625
8 / 8366		0.04456110
730 / 16382		0.03350334
381 / 11372		0.04105166
267 / 6504		0.04831461
43 / 890		0.04632220
5431 / 117244
ESP 0.05585
478 / 8558		 0.06353
277 / 4360		 0.05845
755 / 12918
1KG
 0.05446
44 / 808		 0.06505
86 / 1322		 0.00496
5 / 1008		 0.04908
48 / 978		 0.04467
31 / 694		 0.04040
8 / 198		 0.04433
222 / 5008
View sub-population details for 1000 Genomes (1KG) data
Hide sub-population details for 1000 Genomes (1KG) data

0.04396
8 / 182
British
0.03279
4 / 122
African-American
0.01613
3 / 186
Chinese Dai
0.04651
8 / 172
Bengali
0.04255
8 / 188
Colombian
0.06075
13 / 214
Iberian
0.09375
18 / 192
African-Caribbean
0.00000
0 / 206
Han, Beijing
0.06796
14 / 206
Gujarati Indian
0.00781
1 / 128
Mexican, LA
0.07009
15 / 214
Toscani
0.08081
16 / 198
Esan, Nigeria
0.00000
0 / 208
Japanese
0.05882
12 / 204
Indian Telugu
0.02941
5 / 170
Peruvian
0.04040
8 / 198
Utah Europeans
0.04867
11 / 226
Gambian
0.01010
2 / 198
Kinh, Vietnam
0.03646
7 / 192
Punjabi, Lahore
0.08173
17 / 208
Puerto Rican
0.07071
14 / 198
Luhya, Kenya
0.00000
0 / 210
Southern Han
0.03431
7 / 204
Tamil
0.05294
9 / 170
Mende
0.06481
14 / 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 ENST00000256958 NM_006446.4
Protein ENSP00000256958 Q9Y6L6

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 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.