• Atlas of Cardiac Genetic Variation
• About
•           Inherited Cardiac Conditions          
  • Hypertrophic Cardiomyopathy - HCM
  • Dilated Cardiomyopathy - DCM
  • Arrhythmogenic RV Cardiomyopathy - ARVC
• Gene Quick Link: 
• ABCC9ACTC1ACTN2ANK2ANKRD1CALR3CASQ2CAV3CRYABCSRP3CTF1DESDSC2DSG2DSPDTNAEMDFHL1FHL2FXNGLAJPH2JUPKCNE1KCNE2KCNH2KCNJ2KCNQ1KLF10LAMA4LAMP2LDB3LMNAMYBPC3MYH6MYH7MYL2MYL3MYLK2MYOM1MYOZ2MYPNNEXNOBSCNPDLIM3PKP2PLNPRKAG2RBM20RYR2SCN5ASGCDSRITAZTCAPTGFB3TMEM43TNNC1TNNI3TNNT2TPM1TRIM54TRIM55TRIM63TTNTTRVCL

JPH2 : c.1790C>G

Variant Details

Variant (CDS)	Variant (protein)	Variant Type	Variant Effect	Genomic Location (GRCh37)	ExAC Frequency
c.1790C>G	p.S597W (Ser > Trp)	substitution	missense	chr20:42744525 (reverse strand)	0.00001656

Effect in Cardiac Disease

This variant is considered a rare variant, with a population frequency of 0.00001656 (ExAC mean allelic frequency).

Detection in Population Databases

Database	European	African	East Asian	South Asian	American	Finnish	Other	Total
ExAC	0.00003091 1 / 32354	0.00000000 0 / 3774	0.00000000 0 / 4384	0.00000000 0 / 11724	0.00000000 0 / 5346	0.00000000 0 / 2334	0.00000000 0 / 460	0.00001656 1 / 60376
ESP	0.00000 0 / 8600	0.00000 0 / 4400						0.00000 0 / 13000
1KG	0.00000 0 / 1006	0.00000 0 / 1322	0.00000 0 / 1008	0.00000 0 / 978	0.00000 0 / 694	0.00000 0 / 198		0.00000 0 / 5008

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_394t1	NM_020433.4
Protein	ENSP00000362071	LRG_394p1		Q9BR39

Missense Variant Predictions
SIFT	Grantham	Polyphen-DIV	Polyphen-VAR	Summary 50% of algorithms have predicted that this variant will adversely affect protein function
damaging	radical	possibly damaging	possibly damaging
LRT	MutationTaster	MutationAssessor	FATHMM
unknown	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.