PRDM16 : c.1597T>C

Variant Details

Variant (CDS)	Variant (protein)	Variant Type	Variant Effect	Genomic Location (GRCh37)	ExAC Frequency
c.1597T>C	p.S533P (Ser > Pro)	substitution	missense	chr1:3328358 (forward strand)	0.88968441

Effect in Cardiac Disease

As this variant is present at a population frequency of 0.88968441 (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	0.84043581 55694 / 66268	0.97211279 9377 / 9646	0.99976482 8502 / 8504	0.95077373 15606 / 16414	0.92427926 10644 / 11516	0.90991811 6000 / 6594	0.88727679 795 / 896	0.88968441 106618 / 119838
ESP	0.83559 6902 / 8260	0.96732 3759 / 3886						0.87774 10661 / 12146
1KG	0.81807 661 / 808	0.99244 1312 / 1322	0.99802 1006 / 1008	0.96421 943 / 978	0.90058 625 / 694	0.93939 186 / 198		0.94509 4733 / 5008

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

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

0.84066 153 / 182 British	0.98361 120 / 122 African-American	1.00000 186 / 186 Chinese Dai	0.97093 167 / 172 Bengali	0.87234 164 / 188 Colombian
0.75701 162 / 214 Iberian	0.96875 186 / 192 African-Caribbean	0.99515 205 / 206 Han, Beijing	0.96602 199 / 206 Gujarati Indian	0.88281 113 / 128 Mexican, LA
0.84579 181 / 214 Toscani	1.00000 198 / 198 Esan, Nigeria	1.00000 208 / 208 Japanese	0.95098 194 / 204 Indian Telugu	0.97647 166 / 170 Peruvian
0.83333 165 / 198 Utah Europeans	0.99115 224 / 226 Gambian	0.99495 197 / 198 Kinh, Vietnam	0.96354 185 / 192 Punjabi, Lahore	0.87500 182 / 208 Puerto Rican
	1.00000 198 / 198 Luhya, Kenya	1.00000 210 / 210 Southern Han	0.97059 198 / 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	ENST00000270722		NM_022114.3
Protein	ENSP00000270722			Q9HAZ2

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.