SEPN1 : c.1506C>A

SEPN1 gene summary

Variant Details

Variant (CDS)Variant (protein)Variant Type Variant EffectGenomic Location (GRCh37)ExAC Frequency
c.1506C>Ap.N502K (Asn > Lys)substitutionmissense chr1:26140573 (forward strand)0.77473229

Effect in Cardiac Disease

As this variant is present at a population frequency of 0.77473229 (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
ExAC0.77689954
51799 / 66674		0.29384710
2875 / 9784		0.96427743
8314 / 8622		0.88042161
14534 / 16508		0.89015741
10292 / 11562		0.74863801
4947 / 6608		0.79642058
712 / 894		0.77473229
93473 / 120652
ESP 0.78723
6682 / 8488		 0.32415
1388 / 4282		 0.63195
8070 / 12770
1KG
 0.76980
622 / 808		 0.21180
280 / 1322		 0.96825
976 / 1008		 0.90184
882 / 978		 0.82853
575 / 694		 0.79798
158 / 198		 0.69748
3493 / 5008
View sub-population details for 1000 Genomes (1KG) data
Hide sub-population details for 1000 Genomes (1KG) data

0.75824
138 / 182
British
0.27869
34 / 122
African-American
0.98925
184 / 186
Chinese Dai
0.91860
158 / 172
Bengali
0.83511
157 / 188
Colombian
0.72430
155 / 214
Iberian
0.20312
39 / 192
African-Caribbean
0.96117
198 / 206
Han, Beijing
0.90777
187 / 206
Gujarati Indian
0.89062
114 / 128
Mexican, LA
0.83178
178 / 214
Toscani
0.18182
36 / 198
Esan, Nigeria
0.94231
196 / 208
Japanese
0.93627
191 / 204
Indian Telugu
0.92353
157 / 170
Peruvian
0.76263
151 / 198
Utah Europeans
0.20354
46 / 226
Gambian
0.97980
194 / 198
Kinh, Vietnam
0.87500
168 / 192
Punjabi, Lahore
0.70673
147 / 208
Puerto Rican
0.25758
51 / 198
Luhya, Kenya
0.97143
204 / 210
Southern Han
0.87255
178 / 204
Tamil
0.18824
32 / 170
Mende
0.19444
42 / 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 ENST00000361547 NM_020451.2
Protein ENSP00000355141 Q9NZV5

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
neutral polymorphism (auto) 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.