LDLR : c.1060+10G>C

LDLR gene summary

Variant Details

Variant (CDS)Variant (protein)Variant Type Variant EffectGenomic Location (GRCh37)ExAC Frequency
c.1060+10G>Csubstitutionsplice site chr19:11221457 (forward strand)0.38489054

Effect in Cardiac Disease

As this variant is present at a population frequency of 0.38489054 (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
ExAC0.44314834
29480 / 66524		0.08618688
891 / 10338		0.17026713
1466 / 8610		0.38437765
6343 / 16502		0.41314879
4776 / 11560		0.49425113
3267 / 6610		0.40618102
368 / 906		0.38489054
46591 / 121050
ESP 0.00000
0 / 8600		 0.00000
0 / 4400		 0.00000
0 / 13000
1KG
 0.45173
365 / 808		 0.03101
41 / 1322		 0.18254
184 / 1008		 0.38344
375 / 978		 0.46830
325 / 694		 0.48990
97 / 198		 0.27696
1387 / 5008
View sub-population details for 1000 Genomes (1KG) data
Hide sub-population details for 1000 Genomes (1KG) data

0.45604
83 / 182
British
0.15574
19 / 122
African-American
0.20968
39 / 186
Chinese Dai
0.35465
61 / 172
Bengali
0.46809
88 / 188
Colombian
0.44860
96 / 214
Iberian
0.07292
14 / 192
African-Caribbean
0.16990
35 / 206
Han, Beijing
0.36408
75 / 206
Gujarati Indian
0.42188
54 / 128
Mexican, LA
0.44393
95 / 214
Toscani
0.00000
0 / 198
Esan, Nigeria
0.15385
32 / 208
Japanese
0.40686
83 / 204
Indian Telugu
0.50588
86 / 170
Peruvian
0.45960
91 / 198
Utah Europeans
0.01770
4 / 226
Gambian
0.23737
47 / 198
Kinh, Vietnam
0.41146
79 / 192
Punjabi, Lahore
0.46635
97 / 208
Puerto Rican
0.02020
4 / 198
Luhya, Kenya
0.14762
31 / 210
Southern Han
0.37745
77 / 204
Tamil
0.00000
0 / 170
Mende
0.00000
0 / 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



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.