COL19A1
protein-codingcollagen type XIX alpha 1 chain, the group of Collagens
Gene summary
This gene encodes the alpha chain of type XIX collagen, a member of the FACIT collagen family (fibril-associated collagens with interrupted helices). Although the function of this collagen is not known, other members of this collagen family are found in association with fibril-forming collagens such as type I and II, and serve to maintain the integrity of the extracellular matrix. The transcript produced from this gene has an unusually large 3' UTR which has not been completely sequenced. [provided by RefSeq, Jul 2008]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~345.9 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to COL19A1 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001858.6. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 3 | 2 | 5 | |||
| missense | 182 | 13 | 195 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 3 | 3 | ||||
| Total | 0 | 0 | 188 | 15 | 0 | 203 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001849.2 | 50 | MANE Select | |
| Ensembl | ENSP00000480474.1 | 50 | MANE Select | |
| Ensembl | ENSP00000416556.1 | 3 | Standard | |
| Ensembl | ENSP00000479481.1 | 1 | Standard |
Model Organisms & Knockout Phenotypes
Observed phenotypic effects in mouse and zebrafish models
| Gene / Model | Organism | Observed Phenotype |
|---|---|---|
| col19a1 | Danio rerio | Structure: CaP motoneuron Quality: decreased length abnormal |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Collagen chain trimerization
- Collagen biosynthesis and modifying enzymes
- Collagen formation
- Extracellular matrix organization
- Integrin
Biological Process
- skeletal system development
- cell adhesion
- skeletal muscle tissue development
- cell differentiation
- extracellular matrix organization
Molecular Function
- extracellular matrix structural constituent
- protein binding, bridging
Cellular Component
- extracellular region
- collagen trimer
- extracellular space
- endoplasmic reticulum lumen
- extracellular matrix
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000322773
- Coding exons
- 50
- Length
- 343217
- Individuals with no LoFs
- 125538
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 210
- Defined
- 125748
- p
- 0.000835
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.327 | 609 | 632 | 0.963 | 0.0000323 | 7177 |
| Missense (PolyPhen) | 206 | 242.74 | 0.84863 | 2599 | ||
| Synonymous | -0.415 | 210 | 203 | 1.04 | 0.0000103 | 2313 |
| Loss of Function | 2.12 | 62 | 82.8 | 0.749 | 0.00000417 | 1025 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00056 | 0.00055 | rare |
| Latino/Admixed American | 0.00085 | 0.00075 | rare |
| Ashkenazi Jewish | 0.00020 | 0.00020 | rare |
| East Asian | 0.0013 | 0.0013 | notable |
| Finnish | 0.00074 | 0.00074 | rare |
| European (Non-Finnish) | 0.00088 | 0.00087 | rare |
| South Asian | 0.0011 | 0.0011 | notable |
| Other | 0.00049 | 0.00033 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: May act as a cross-bridge between fibrils and other extracellular matrix molecules. Involved in skeletal myogenesis in the developing esophagus. May play a role in organization of the pericellular matrix or the sphinteric smooth muscle. {ECO:0000269|PubMed:12788917}.;
Recessive Scores
- pRec
- 0.126
Intolerance Scores
- LoFtool
- 0.148
- RVIS EVS
- -0.12
- RVIS percentile EVS
- 44.12
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.0708
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | High |
| Cancer | Medium | Medium | Medium |