PCSK9 : c.658-7C>T

PCSK9 gene summary

Variant Details

Variant (CDS)Variant (protein)Variant Type Variant EffectGenomic Location (GRCh37)ExAC Frequency
c.658-7C>Tsubstitutionsplice site chr1:55518316 (forward strand)0.42759317

Effect in Cardiac Disease

As this variant is present at a population frequency of 0.42759317 (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
ExAC0.45486997
29945 / 65832		0.49712530
5015 / 10088		0.22564103
1936 / 8580		0.44761847
7349 / 16418		0.31342119
3615 / 11534		0.46043385
3014 / 6546		0.43736018
391 / 894		0.42759317
51265 / 119892
ESP 0.44465
3824 / 8600		 0.48457
2135 / 4406		 0.45817
5959 / 13006
1KG
 0.45050
364 / 808		 0.50530
668 / 1322		 0.19643
198 / 1008		 0.43967
430 / 978		 0.32421
225 / 694		 0.44949
89 / 198		 0.39417
1974 / 5008
View sub-population details for 1000 Genomes (1KG) data
Hide sub-population details for 1000 Genomes (1KG) data

0.42857
78 / 182
British
0.43443
53 / 122
African-American
0.17204
32 / 186
Chinese Dai
0.38953
67 / 172
Bengali
0.32447
61 / 188
Colombian
0.43458
93 / 214
Iberian
0.46875
90 / 192
African-Caribbean
0.21845
45 / 206
Han, Beijing
0.44660
92 / 206
Gujarati Indian
0.34375
44 / 128
Mexican, LA
0.46262
99 / 214
Toscani
0.58081
115 / 198
Esan, Nigeria
0.21154
44 / 208
Japanese
0.51471
105 / 204
Indian Telugu
0.22353
38 / 170
Peruvian
0.47475
94 / 198
Utah Europeans
0.62832
142 / 226
Gambian
0.17677
35 / 198
Kinh, Vietnam
0.39062
75 / 192
Punjabi, Lahore
0.39423
82 / 208
Puerto Rican
0.40909
81 / 198
Luhya, Kenya
0.20000
42 / 210
Southern Han
0.44608
91 / 204
Tamil
0.47059
80 / 170
Mende
0.49537
107 / 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 ENST00000302118 LRG_275t1NM_174936.3
Protein ENSP00000303208 LRG_275p1Q8NBP7



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.