JPH2 : c.1186G>A

JPH2 gene summary

Variant Details

Variant (CDS)Variant (protein)Variant Type Variant EffectGenomic Location (GRCh37)ExAC Frequency
c.1186G>Ap.A396T (Ala > Thr)substitutionmissense chr20:42747247 (reverse strand)0.18457619

Effect in Cardiac Disease

As this variant is present at a population frequency of 0.18457619 (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
ExAC0.13623223
9048 / 66416		0.34379224
3561 / 10358		0.37135526
3184 / 8574		0.28111744
4639 / 16502		0.09066505
1047 / 11548		0.10233121
676 / 6606		0.17888889
161 / 900		0.18457619
22316 / 120904
ESP 0.12895
1109 / 8600		 0.33023
1455 / 4406		 0.19714
2564 / 13006
1KG
 0.12871
104 / 808		 0.39334
520 / 1322		 0.35714
360 / 1008		 0.29346
287 / 978		 0.10086
70 / 694		 0.06566
13 / 198		 0.27037
1354 / 5008
View sub-population details for 1000 Genomes (1KG) data
Hide sub-population details for 1000 Genomes (1KG) data

0.09890
18 / 182
British
0.35246
43 / 122
African-American
0.27957
52 / 186
Chinese Dai
0.31395
54 / 172
Bengali
0.10638
20 / 188
Colombian
0.16355
35 / 214
Iberian
0.41146
79 / 192
African-Caribbean
0.34466
71 / 206
Han, Beijing
0.31068
64 / 206
Gujarati Indian
0.07812
10 / 128
Mexican, LA
0.13084
28 / 214
Toscani
0.43939
87 / 198
Esan, Nigeria
0.48558
101 / 208
Japanese
0.27451
56 / 204
Indian Telugu
0.05882
10 / 170
Peruvian
0.11616
23 / 198
Utah Europeans
0.37168
84 / 226
Gambian
0.31818
63 / 198
Kinh, Vietnam
0.29167
56 / 192
Punjabi, Lahore
0.14423
30 / 208
Puerto Rican
0.41919
83 / 198
Luhya, Kenya
0.34762
73 / 210
Southern Han
0.27941
57 / 204
Tamil
0.34706
59 / 170
Mende
0.39352
85 / 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 ENST00000372980 LRG_394t1NM_020433.4
Protein ENSP00000362071 LRG_394p1Q9BR39

Missense Variant Predictions
SIFT Grantham Polyphen-DIV Polyphen-VAR Summary
25% of algorithms have predicted that this variant will adversely affect protein function
tolerated moderately conservative probably damaging probably damaging
LRT MutationTaster MutationAssessor FATHMM
neutral polymorphism (auto) low impact 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.