SYNE1 : c.8405C>T

Variant Details

Variant (CDS)	Variant (protein)	Variant Type	Variant Effect	Genomic Location (GRCh37)	ExAC Frequency
c.8405C>T	p.A2802V (Ala > Val)	substitution	missense	chr6:152708310 (reverse strand)	0.23728534

Effect in Cardiac Disease

As this variant is present at a population frequency of 0.23728534 (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	0.22288832 14872 / 66724	0.14597348 1519 / 10406	0.41857772 3614 / 8634	0.31144761 5142 / 16510	0.18578101 2148 / 11562	0.19147005 1266 / 6612	0.25881057 235 / 908	0.23728534 28796 / 121356
ESP	0.21895 1883 / 8600	0.15842 698 / 4406						0.19845 2581 / 13006
1KG	0.22030 178 / 808	0.15204 201 / 1322	0.40179 405 / 1008	0.31800 311 / 978	0.16138 112 / 694	0.20202 40 / 198		0.24900 1247 / 5008

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

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

0.18681 34 / 182 British	0.11475 14 / 122 African-American	0.36022 67 / 186 Chinese Dai	0.26163 45 / 172 Bengali	0.21277 40 / 188 Colombian
0.19626 42 / 214 Iberian	0.15104 29 / 192 African-Caribbean	0.42718 88 / 206 Han, Beijing	0.30583 63 / 206 Gujarati Indian	0.17969 23 / 128 Mexican, LA
0.28972 62 / 214 Toscani	0.18687 37 / 198 Esan, Nigeria	0.45673 95 / 208 Japanese	0.33333 68 / 204 Indian Telugu	0.08824 15 / 170 Peruvian
0.20202 40 / 198 Utah Europeans	0.15487 35 / 226 Gambian	0.36364 72 / 198 Kinh, Vietnam	0.32292 62 / 192 Punjabi, Lahore	0.16346 34 / 208 Puerto Rican
	0.12121 24 / 198 Luhya, Kenya	0.39524 83 / 210 Southern Han	0.35784 73 / 204 Tamil
	0.14706 25 / 170 Mende
	0.17130 37 / 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 0% of algorithms have predicted that this variant will adversely affect protein function
tolerated	moderately conservative	benign	benign
LRT	MutationTaster	MutationAssessor	FATHMM
neutral	polymorphism (auto)	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.