SYNE1 : c.21691T>G

SYNE1 gene summary

Variant Details

Variant (CDS)Variant (protein)Variant Type Variant EffectGenomic Location (GRCh37)ExAC Frequency
c.21691T>Gp.F7231V (Phe > Val)substitutionmissense chr6:152540278 (reverse strand)0.99228184

Effect in Cardiac Disease

As this variant is present at a population frequency of 0.99228184 (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
ExAC0.98864215
65980 / 66738		0.99807803
10386 / 10406		1.00000000
8648 / 8648		0.99878876
16492 / 16512		0.99464409
11514 / 11576		0.98911400
6542 / 6614		0.99449339
903 / 908		0.99228184
120465 / 121402
ESP 0.99012
8515 / 8600		 0.99887
4401 / 4406		 0.99308
12916 / 13006
1KG
 0.98515
796 / 808		 0.99924
1321 / 1322		 1.00000
1008 / 1008		 1.00000
978 / 978		 0.98991
687 / 694		 0.98990
196 / 198		 0.99561
4986 / 5008
View sub-population details for 1000 Genomes (1KG) data
Hide sub-population details for 1000 Genomes (1KG) data

0.98901
180 / 182
British
1.00000
122 / 122
African-American
1.00000
186 / 186
Chinese Dai
1.00000
172 / 172
Bengali
0.99468
187 / 188
Colombian
0.98131
210 / 214
Iberian
0.99479
191 / 192
African-Caribbean
1.00000
206 / 206
Han, Beijing
1.00000
206 / 206
Gujarati Indian
1.00000
128 / 128
Mexican, LA
0.98598
211 / 214
Toscani
1.00000
198 / 198
Esan, Nigeria
1.00000
208 / 208
Japanese
1.00000
204 / 204
Indian Telugu
0.98235
167 / 170
Peruvian
0.98485
195 / 198
Utah Europeans
1.00000
226 / 226
Gambian
1.00000
198 / 198
Kinh, Vietnam
1.00000
192 / 192
Punjabi, Lahore
0.98558
205 / 208
Puerto Rican
1.00000
198 / 198
Luhya, Kenya
1.00000
210 / 210
Southern Han
1.00000
204 / 204
Tamil
1.00000
170 / 170
Mende
1.00000
216 / 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_427t2NM_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 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.