COL11A1 : c.4603T>C

Variant Details

Variant (CDS)	Variant (protein)	Variant Type	Variant Effect	Genomic Location (GRCh37)	ExAC Frequency
c.4603T>C	p.S1535P (Ser > Pro)	substitution	missense	chr1:103354138 (reverse strand)	0.79415508

Effect in Cardiac Disease

As this variant is present at a population frequency of 0.79415508 (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	0.80875638 53847 / 66580	0.81032809 8348 / 10302	0.73035010 6300 / 8626	0.67062386 11072 / 16510	0.87809341 10077 / 11476	0.86336063 5693 / 6594	0.82891832 751 / 906	0.79415508 96088 / 120994
ESP	0.81128 6977 / 8600	0.79868 3519 / 4406						0.80701 10496 / 13006
1KG	0.83045 671 / 808	0.80484 1064 / 1322	0.74802 754 / 1008	0.66155 647 / 978	0.89481 621 / 694	0.82828 164 / 198		0.78295 3921 / 5008

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

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

0.80769 147 / 182 British	0.76230 93 / 122 African-American	0.78495 146 / 186 Chinese Dai	0.66279 114 / 172 Bengali	0.89894 169 / 188 Colombian
0.85047 182 / 214 Iberian	0.84896 163 / 192 African-Caribbean	0.75243 155 / 206 Han, Beijing	0.68932 142 / 206 Gujarati Indian	0.86719 111 / 128 Mexican, LA
0.86449 185 / 214 Toscani	0.83333 165 / 198 Esan, Nigeria	0.76442 159 / 208 Japanese	0.56863 116 / 204 Indian Telugu	0.95294 162 / 170 Peruvian
0.79293 157 / 198 Utah Europeans	0.76991 174 / 226 Gambian	0.69192 137 / 198 Kinh, Vietnam	0.73438 141 / 192 Punjabi, Lahore	0.86058 179 / 208 Puerto Rican
	0.76263 151 / 198 Luhya, Kenya	0.74762 157 / 210 Southern Han	0.65686 134 / 204 Tamil
	0.80000 136 / 170 Mende
	0.84259 182 / 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	ENST00000370096		NM_001854.3
Protein	ENSP00000359114			P12107

Missense Variant Predictions
SIFT	Grantham	Polyphen-DIV	Polyphen-VAR	Summary 12.5% 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	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.