PCSK9 : c.799+3A>G

PCSK9 gene summary

Variant Details

Variant (CDS)Variant (protein)Variant Type Variant EffectGenomic Location (GRCh37)ExAC Frequency
c.799+3A>Gsubstitutionsplice site chr1:55518467 (forward strand)0.43114685

Effect in Cardiac Disease

As this variant is present at a population frequency of 0.43114685 (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
ExAC0.41522336
26899 / 64782		0.71942948
7213 / 10026		0.26304704
2248 / 8546		0.49065761
8088 / 16484		0.30354968
3489 / 11494		0.44418960
2905 / 6540		0.40653153
361 / 888		0.43114685
51203 / 118760
ESP 0.40195
3456 / 8598		 0.70359
3100 / 4406		 0.50415
6556 / 13004
1KG
 0.39604
320 / 808		 0.75265
995 / 1322		 0.22718
229 / 1008		 0.51329
502 / 978		 0.29827
207 / 694		 0.41414
82 / 198		 0.46625
2335 / 5008
View sub-population details for 1000 Genomes (1KG) data
Hide sub-population details for 1000 Genomes (1KG) data

0.40659
74 / 182
British
0.62295
76 / 122
African-American
0.18280
34 / 186
Chinese Dai
0.44767
77 / 172
Bengali
0.31915
60 / 188
Colombian
0.39720
85 / 214
Iberian
0.70312
135 / 192
African-Caribbean
0.24272
50 / 206
Han, Beijing
0.52913
109 / 206
Gujarati Indian
0.29688
38 / 128
Mexican, LA
0.41121
88 / 214
Toscani
0.81313
161 / 198
Esan, Nigeria
0.24038
50 / 208
Japanese
0.55392
113 / 204
Indian Telugu
0.22941
39 / 170
Peruvian
0.36869
73 / 198
Utah Europeans
0.83186
188 / 226
Gambian
0.21212
42 / 198
Kinh, Vietnam
0.48958
94 / 192
Punjabi, Lahore
0.33654
70 / 208
Puerto Rican
0.68182
135 / 198
Luhya, Kenya
0.25238
53 / 210
Southern Han
0.53431
109 / 204
Tamil
0.74706
127 / 170
Mende
0.80093
173 / 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.