COL1A1 : c.1300-8C>T

COL1A1 gene summary

Variant Details

Variant (CDS)Variant (protein)Variant Type Variant EffectGenomic Location (GRCh37)ExAC Frequency
c.1300-8C>Tsubstitutionsplice site chr17:48272469 (reverse strand)0.00841046

Effect in Cardiac Disease

As this variant is present at a population frequency of 0.00841046 (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
ExAC0.00150689
100 / 66362		0.07950804
821 / 10326		0.00057964
5 / 8626		0.00254484
42 / 16504		0.00338307
39 / 11528		0.00015244
1 / 6560		0.00892857
8 / 896		0.00841046
1016 / 120802
ESP 0.00000
0 / 8600		 0.00000
0 / 4400		 0.00000
0 / 13000
1KG
 0.00000
0 / 1004		 0.11566
127 / 1098		 0.00000
0 / 1008		 0.00428
4 / 934		 0.00290
2 / 690		 0.00000
0 / 197		 0.02809
133 / 4734
View sub-population details for 1000 Genomes (1KG) data
Hide sub-population details for 1000 Genomes (1KG) data

0.00000
0 / 182
British
0.08108
9 / 111
African-American
0.00000
0 / 186
Chinese Dai
0.00000
0 / 170
Bengali
0.00000
0 / 185
Colombian
0.00000
0 / 213
Iberian
0.12575
21 / 167
African-Caribbean
0.00000
0 / 206
Han, Beijing
0.00000
0 / 194
Gujarati Indian
0.00781
1 / 128
Mexican, LA
0.00000
0 / 214
Toscani
0.17500
28 / 160
Esan, Nigeria
0.00000
0 / 208
Japanese
0.00000
0 / 192
Indian Telugu
0.00000
0 / 170
Peruvian
0.00000
0 / 198
Utah Europeans
0.10857
19 / 175
Gambian
0.00000
0 / 198
Kinh, Vietnam
0.01648
3 / 182
Punjabi, Lahore
0.00483
1 / 207
Puerto Rican
0.09494
15 / 158
Luhya, Kenya
0.00000
0 / 210
Southern Han
0.00510
1 / 196
Tamil
0.07586
11 / 145
Mende
0.13187
24 / 182
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 ENST00000225964 NM_000088.3
Protein ENSP00000225964 P02452



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.