LOX : c.473G>A

Variant Details

Variant (CDS)	Variant (protein)	Variant Type	Variant Effect	Genomic Location (GRCh37)	ExAC Frequency
c.473G>A	p.R158Q (Arg > Gln)	substitution	missense	chr5:121413208 (reverse strand)	0.17280773

Effect in Cardiac Disease

As this variant is present at a population frequency of 0.17280773 (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	0.17056482 11143 / 65330	0.17707246 1696 / 9578	0.20236147 1731 / 8554	0.17187879 2836 / 16500	0.17842215 2049 / 11484	0.14156719 925 / 6534	0.18161435 162 / 892	0.17280773 20542 / 118872
ESP	0.17376 1494 / 8598	0.17842 784 / 4394						0.17534 2278 / 12992
1KG	0.16213 131 / 808	0.14372 190 / 1322	0.18750 189 / 1008	0.13497 132 / 978	0.15994 111 / 694	0.16162 32 / 198		0.15675 785 / 5008

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

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

0.15385 28 / 182 British	0.17213 21 / 122 African-American	0.15591 29 / 186 Chinese Dai	0.13372 23 / 172 Bengali	0.14362 27 / 188 Colombian
0.15421 33 / 214 Iberian	0.10938 21 / 192 African-Caribbean	0.19417 40 / 206 Han, Beijing	0.10680 22 / 206 Gujarati Indian	0.19531 25 / 128 Mexican, LA
0.18224 39 / 214 Toscani	0.13636 27 / 198 Esan, Nigeria	0.17308 36 / 208 Japanese	0.15196 31 / 204 Indian Telugu	0.10000 17 / 170 Peruvian
0.15657 31 / 198 Utah Europeans	0.12389 28 / 226 Gambian	0.18182 36 / 198 Kinh, Vietnam	0.16146 31 / 192 Punjabi, Lahore	0.20192 42 / 208 Puerto Rican
	0.15657 31 / 198 Luhya, Kenya	0.22857 48 / 210 Southern Han	0.12255 25 / 204 Tamil
	0.21176 36 / 170 Mende
	0.12037 26 / 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	ENST00000231004		NM_002317.5
Protein	ENSP00000231004			P28300

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)	low impact	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.