KCNQ2 : c.2339A>C

Variant Details

Variant (CDS)	Variant (protein)	Variant Type	Variant Effect	Genomic Location (GRCh37)	ExAC Frequency
c.2339A>C	p.N780T (Asn > Thr)	substitution	missense	chr20:62038277 (reverse strand)	0.63723962

Effect in Cardiac Disease

As this variant is present at a population frequency of 0.63723962 (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	0.66842876 37428 / 55994	0.53178906 4316 / 8116	0.64318304 4793 / 7452	0.62566631 9390 / 15008	0.53372434 5096 / 9548	0.69054945 3142 / 4550	0.61602210 446 / 724	0.63723962 64611 / 101392
ESP	0.64387 5527 / 8584	0.50985 2225 / 4364						0.59870 7752 / 12948
1KG	0.61881 500 / 808	0.46293 612 / 1322	0.66865 674 / 1008	0.66053 646 / 978	0.55187 383 / 694	0.71717 142 / 198		0.59046 2957 / 5008

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

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

0.63187 115 / 182 British	0.48361 59 / 122 African-American	0.74194 138 / 186 Chinese Dai	0.68605 118 / 172 Bengali	0.64362 121 / 188 Colombian
0.60280 129 / 214 Iberian	0.49479 95 / 192 African-Caribbean	0.61650 127 / 206 Han, Beijing	0.63592 131 / 206 Gujarati Indian	0.57031 73 / 128 Mexican, LA
0.60280 129 / 214 Toscani	0.46465 92 / 198 Esan, Nigeria	0.66346 138 / 208 Japanese	0.67157 137 / 204 Indian Telugu	0.49412 84 / 170 Peruvian
0.64141 127 / 198 Utah Europeans	0.45133 102 / 226 Gambian	0.71212 141 / 198 Kinh, Vietnam	0.65625 126 / 192 Punjabi, Lahore	0.50481 105 / 208 Puerto Rican
	0.42929 85 / 198 Luhya, Kenya	0.61905 130 / 210 Southern Han	0.65686 134 / 204 Tamil
	0.48824 83 / 170 Mende
	0.44444 96 / 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	ENST00000359125		NM_172107.2
Protein	ENSP00000352035			O43526

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.