SCO2 : c.59G>C

Variant Details

Variant (CDS)	Variant (protein)	Variant Type	Variant Effect	Genomic Location (GRCh37)	ExAC Frequency
c.59G>C	p.R20P (Arg > Pro)	substitution	missense	chr22:50962782 (reverse strand)	0.63925553

Effect in Cardiac Disease

As this variant is present at a population frequency of 0.63925553 (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	0.61598258 38749 / 62906	0.65130704 5880 / 9028	0.69890424 5868 / 8396	0.68456170 11183 / 16336	0.63679494 7248 / 11382	0.65513563 4299 / 6562	0.68384075 584 / 854	0.63925553 73811 / 115464
ESP	0.61699 5279 / 8556	0.65734 2891 / 4398						0.63069 8170 / 12954
1KG	0.61510 497 / 808	0.65582 867 / 1322	0.66766 673 / 1008	0.68609 671 / 978	0.61960 430 / 694	0.63131 125 / 198		0.65156 3263 / 5008

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

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

0.60440 110 / 182 British	0.68852 84 / 122 African-American	0.61828 115 / 186 Chinese Dai	0.73837 127 / 172 Bengali	0.59574 112 / 188 Colombian
0.65421 140 / 214 Iberian	0.64062 123 / 192 African-Caribbean	0.73786 152 / 206 Han, Beijing	0.70874 146 / 206 Gujarati Indian	0.60156 77 / 128 Mexican, LA
0.57944 124 / 214 Toscani	0.63131 125 / 198 Esan, Nigeria	0.68269 142 / 208 Japanese	0.64706 132 / 204 Indian Telugu	0.67647 115 / 170 Peruvian
0.62121 123 / 198 Utah Europeans	0.71239 161 / 226 Gambian	0.62121 123 / 198 Kinh, Vietnam	0.65625 126 / 192 Punjabi, Lahore	0.60577 126 / 208 Puerto Rican
	0.66162 131 / 198 Luhya, Kenya	0.67143 141 / 210 Southern Han	0.68627 140 / 204 Tamil
	0.67647 115 / 170 Mende
	0.59259 128 / 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	ENST00000395693		NM_005138.2
Protein	ENSP00000379046			O43819

Missense Variant Predictions
SIFT	Grantham	Polyphen-DIV	Polyphen-VAR	Summary 25% of algorithms have predicted that this variant will adversely affect protein function
tolerated	moderately radical	benign	benign
LRT	MutationTaster	MutationAssessor	FATHMM
neutral	polymorphism (auto)	neutral	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.