MYL3 : c.61C>T

Variant Details

Variant (CDS)	Variant (protein)	Variant Type	Variant Effect	Genomic Location (GRCh37)	ExAC Frequency
c.61C>T	p.P21S (Pro > Ser)	substitution	missense	chr3:46904820 (reverse strand)	0.00000824

Effect in Cardiac Disease

This variant is considered a rare variant, with a population frequency of 0.00000824 (ExAC mean allelic frequency).

HCM	Rare MYL3 Non-Truncating* variants are significantly enriched in HCM (details) and have an etiological fraction (EF) of 0.80.* OMGL: Detected in 0 / 1535 HCM patients. LMM: Detected in 0 / 2650 HCM patients.
DCM	There is no significant excess of rare MYL3 Non-Truncating variants in DCM (details). OMGL: Detected in 0 / 355 DCM patients. LMM: Detected in 0 / 188 DCM patients.

HCM

Rare MYL3 Non-Truncating variants are significantly enriched in HCM (details) and have an etiological fraction (EF) of 0.80.

OMGL: Detected in 0 / 1535 HCM patients.

LMM: Detected in 0 / 2650 HCM patients.

DCM

There is no significant excess of rare MYL3 Non-Truncating variants in DCM (details).

OMGL: Detected in 0 / 355 DCM patients.

LMM: Detected in 0 / 188 DCM patients.

The EF is the estimated proportion of rare variants of this class that will be pathogenic in a cardiomyopathy proband, a prior probability based solely on variant frequency data in cases and controls, and should be further refined by additional evidence such as family segregation data, known association with disease, population frequency, protein domain analysis, functional studies and in silico algorithms to assess the significance of a variant.

For more information on the clinical significance of this variant, please see the ClinVar entry.

Detection in Population Databases

Database	European	African	East Asian	South Asian	American	Finnish	Other	Total
ExAC	0.00001499 1 / 66694	0.00000000 0 / 10394	0.00000000 0 / 8646	0.00000000 0 / 16512	0.00000000 0 / 11574	0.00000000 0 / 6614	0.00000000 0 / 906	0.00000824 1 / 121340
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	ENST00000395869	LRG_395t1	NM_000258.2
Protein	ENSP00000379210	LRG_395p1		P08590

Missense Variant Predictions
SIFT	Grantham	Polyphen-DIV	Polyphen-VAR	Summary 12.5% of algorithms have predicted that this variant will adversely affect protein function
tolerated	moderately conservative	benign	benign
LRT	MutationTaster	MutationAssessor	FATHMM
unknown	polymorphism	low impact	damaging

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.