LIPC : c.644A>G

Variant Details

Variant (CDS)	Variant (protein)	Variant Type	Variant Effect	Genomic Location (GRCh37)	ExAC Frequency
c.644A>G	p.N215S (Asn > Ser)	substitution	missense	chr15:58838010 (forward strand)	0.47025339

Effect in Cardiac Disease

As this variant is present at a population frequency of 0.47025339 (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	0.35547531 23723 / 66736	0.67249664 6998 / 10406	0.83117484 7188 / 8648	0.55160509 9107 / 16510	0.55918438 6472 / 11574	0.48684211 3219 / 6612	0.41721854 378 / 906	0.47025339 57085 / 121392
ESP	0.36312 3117 / 8584	0.67838 2974 / 4384						0.46970 6091 / 12968
1KG	0.37005 299 / 808	0.71407 944 / 1322	0.79167 798 / 1008	0.58998 577 / 978	0.49280 342 / 694	0.44444 88 / 198		0.60863 3048 / 5008

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

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

0.41758 76 / 182 British	0.72131 88 / 122 African-American	0.69355 129 / 186 Chinese Dai	0.67442 116 / 172 Bengali	0.41489 78 / 188 Colombian
0.41589 89 / 214 Iberian	0.68750 132 / 192 African-Caribbean	0.77670 160 / 206 Han, Beijing	0.54854 113 / 206 Gujarati Indian	0.57031 73 / 128 Mexican, LA
0.29907 64 / 214 Toscani	0.75758 150 / 198 Esan, Nigeria	0.94231 196 / 208 Japanese	0.54412 111 / 204 Indian Telugu	0.60588 103 / 170 Peruvian
0.35354 70 / 198 Utah Europeans	0.76106 172 / 226 Gambian	0.72222 143 / 198 Kinh, Vietnam	0.58854 113 / 192 Punjabi, Lahore	0.42308 88 / 208 Puerto Rican
	0.71717 142 / 198 Luhya, Kenya	0.80952 170 / 210 Southern Han	0.60784 124 / 204 Tamil
	0.69412 118 / 170 Mende
	0.65741 142 / 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	ENST00000299022		NM_000236.2
Protein	ENSP00000299022			P11150

Missense Variant Predictions
SIFT	Grantham	Polyphen-DIV	Polyphen-VAR	Summary 25% of algorithms have predicted that this variant will adversely affect protein function
damaging	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.