| Variant ID | 590 |
|---|---|
| Entrez Gene ID | 1277 |
| Gene | COL1A1 (GeneCards) |
| Location | hg19 17:48271508-48271508
hg38 17:50194147-50194147 |
| Disease | Osteogenesis imperfecta type2 (view all the variants in this disease) |
| Method | Allele Specific Oligohibridization |
| Mutation(HGVS format) | NC_000017.10:g.48271508 C>T (Genome Assembly: hg19) |
| Exon or Intron | Exon |
|---|---|
| Position in protein | 551 |
| Amino acid changes in protein | G > R |
| Position in cDNA | 1651 |
| Changes in cDNA | G > A |
| mRNA accession | NM_000088.3 |
| mRNA length | 4395 |
| Reference length | 81195210 |
| MAF in gnomAD genome (version 2.0.1) | 0 |
|---|---|
| EIGEN score | 0.9151 |
| CADD Raw score (version 1.3) | 5.820284 (Deleterious) |
| FATHMM raw prediction score | 0.98033 (Tolerated) |
| SIFT score | 0 (Deleterious) |
| LRT score | 0 (Deleterious) |
| MutationTaster score | 1 (Deleterious) |
| MutatioinAssessor score | 3.68 (Deleterious) |
| PROVEAN score | -4.73 (Deleterious) |
| MetaSVM score | 1.046 (Deleterious) |
| MetaLR score | 0.981 (Deleterious) |
| MCAP score | 0.866 (Deleterious) |
| FitCons score | 0.707 (Highly Significant p < 0.003 ) |
| Genomic Evolutionary Rate Profiling (GERP) score | 4.29 |
| PhyloP score based on multiple alignment of 100 vertebrates | 7.867 |
| PhastCons score based on multiple alignment of 100 vertebrates | 1 |
| SiPhy log transformed odds ratio on multiple alignment of 29 mammals | 15.673 |
| Deleterious probability by iFish2 | 0.9875 (Deleterious) |
| Deleterious probability by DeFine | 0.9768 (Deleterious) |
| Entrez Gene ID | 1277 (NCBI Gene) |
|---|---|
| Official Gene Symbol | COL1A1 (GeneCards) |
| Number of variants in COL1A1 in this database | 15 (view all the variants) |
| Full name | collagen type I alpha 1 chain |
| Band | 17q21.33 |
| Other IDs | Vega: OTTHUMG00000148674 OMIM: 120150 HGNC: HGNC:2197 Ensembl: ENSG00000108821 |
| Other names | OI1, OI2, OI3, OI4, EDSC, EDSARTH1 |
| Summary | This gene encodes the pro-alpha1 chains of type I collagen whose triple helix comprises two alpha1 chains and one alpha2 chain. Type I is a fibril-forming collagen found in most connective tissues and is abundant in bone, cornea, dermis and tendon. Mutations in this gene are associated with osteogenesis imperfecta types I-IV, Ehlers-Danlos syndrome type VIIA, Ehlers-Danlos syndrome Classical type, Caffey Disease and idiopathic osteoporosis. Reciprocal translocations between chromosomes 17 and 22, where this gene and the gene for platelet-derived growth factor beta are located, are associated with a particular type of skin tumor called dermatofibrosarcoma protuberans, resulting from unregulated expression of the growth factor. Two transcripts, resulting from the use of alternate polyadenylation signals, have been identified for this gene. [provided by R. Dalgleish, Feb 2008] |
| Individual ID | 2339700.01 (view all the variants in this individual) |
|---|---|
| Pubmed ID | 2339700 |
| Whose mosaic mutation | Father |
| Phenotype | 1 |
| Number of affected children | 1 ( male: 1; ) |
| Disease | Osteogenesis imperfecta type2 (view all the variants in this disease) |
| OMIM ID | 166210 |
| Pubmed ID | 2339700 |
|---|---|
| Title | Variable expression of osteogenesis imperfecta in a nuclear family is explained by somatic mosaicism for a lethal point mutation in the alpha 1(I) gene (COL1A1) of type I collagen in a parent |
| Journal | American Journal of Human Genetics |
| Publication date | 1990.06 |
| Disease | Osteogenesis imperfecta type2 |
| Number of cases | Male cases: 1; |