SYNE1 : c.3125T>C

Variant Details

Variant (CDS)	Variant (protein)	Variant Type	Variant Effect	Genomic Location (GRCh37)	ExAC Frequency
c.3125T>C	p.V1042A (Val > Ala)	substitution	missense	chr6:152772264 (reverse strand)	0.48114949

Effect in Cardiac Disease

As this variant is present at a population frequency of 0.48114949 (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
ExAC	0.42911521 28634 / 66728	0.74860657 7790 / 10406	0.75688498 6541 / 8642	0.51962209 8580 / 16512	0.31964378 3697 / 11566	0.40792259 2698 / 6614	0.50660793 460 / 908	0.48114949 58400 / 121376
ESP	0.42954 3694 / 8600	0.73355 3232 / 4406						0.53252 6926 / 13006
1KG	0.45916 371 / 808	0.80862 1069 / 1322	0.74901 755 / 1008	0.51943 508 / 978	0.37320 259 / 694	0.39899 79 / 198		0.60723 3041 / 5008

View sub-population details for 1000 Genomes (1KG) data

Hide sub-population details for 1000 Genomes (1KG) data

0.41758 76 / 182 British	0.68852 84 / 122 African-American	0.75269 140 / 186 Chinese Dai	0.55814 96 / 172 Bengali	0.39362 74 / 188 Colombian
0.52336 112 / 214 Iberian	0.81771 157 / 192 African-Caribbean	0.72816 150 / 206 Han, Beijing	0.50485 104 / 206 Gujarati Indian	0.29688 38 / 128 Mexican, LA
0.50467 108 / 214 Toscani	0.83838 166 / 198 Esan, Nigeria	0.75962 158 / 208 Japanese	0.53431 109 / 204 Indian Telugu	0.25882 44 / 170 Peruvian
0.37879 75 / 198 Utah Europeans	0.80088 181 / 226 Gambian	0.79293 157 / 198 Kinh, Vietnam	0.45833 88 / 192 Punjabi, Lahore	0.49519 103 / 208 Puerto Rican
	0.82828 164 / 198 Luhya, Kenya	0.71429 150 / 210 Southern Han	0.54412 111 / 204 Tamil
	0.82353 140 / 170 Mende
	0.81944 177 / 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	ENST00000423061	LRG_427t2	NM_033071.3
Protein	ENSP00000396024	LRG_427p2

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	benign	benign
LRT	MutationTaster	MutationAssessor	FATHMM
neutral	polymorphism (auto)	medium 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.