COL1A1 : c.3223A>G

COL1A1 gene summary

Variant Details

Variant (CDS)Variant (protein)Variant Type Variant EffectGenomic Location (GRCh37)ExAC Frequency
c.3223A>Gp.T1075A (Ala > Ala)substitutionmissense chr17:48265495 (reverse strand)0.98479442

Effect in Cardiac Disease

As this variant is present at a population frequency of 0.98479442 (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
ExAC0.98585867
24191 / 24538		0.94566570
4560 / 4822		1.00000000
2980 / 2980		0.99583719
10765 / 10810		0.98941799
2992 / 3024		0.97633873
1568 / 1606		0.97887324
417 / 426		0.98479442
47473 / 48206
ESP 0.00000
0 / 8600		 0.00000
0 / 4400		 0.00000
0 / 13000
1KG
 0.97896
791 / 808		 0.94402
1248 / 1322		 1.00000
1008 / 1008		 0.99693
975 / 978		 0.99424
690 / 694		 0.95960
190 / 198		 0.97883
4902 / 5008
View sub-population details for 1000 Genomes (1KG) data
Hide sub-population details for 1000 Genomes (1KG) data

0.97802
178 / 182
British
0.94262
115 / 122
African-American
1.00000
186 / 186
Chinese Dai
1.00000
172 / 172
Bengali
0.98404
185 / 188
Colombian
0.99533
213 / 214
Iberian
0.94792
182 / 192
African-Caribbean
1.00000
206 / 206
Han, Beijing
0.99515
205 / 206
Gujarati Indian
1.00000
128 / 128
Mexican, LA
0.97664
209 / 214
Toscani
0.92929
184 / 198
Esan, Nigeria
1.00000
208 / 208
Japanese
1.00000
204 / 204
Indian Telugu
1.00000
170 / 170
Peruvian
0.96465
191 / 198
Utah Europeans
0.95575
216 / 226
Gambian
1.00000
198 / 198
Kinh, Vietnam
0.99479
191 / 192
Punjabi, Lahore
0.99519
207 / 208
Puerto Rican
0.94444
187 / 198
Luhya, Kenya
1.00000
210 / 210
Southern Han
0.99510
203 / 204
Tamil
0.94118
160 / 170
Mende
0.94444
204 / 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 ENST00000225964 NM_000088.3
Protein ENSP00000225964 P02452

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 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.