COL14A1
protein-codingcollagen type XIV alpha 1 chain, the group of Fibronectin type III domain containing|Collagens
Gene summary
This gene encodes the alpha chain of type XIV collagen, a member of the FACIT (fibril-associated collagens with interrupted triple helices) collagen family. Type XIV collagen interacts with the fibril surface and is involved in the regulation of fibrillogenesis. [provided by RefSeq, Jan 2013]
- UND
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~313.8 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AD
Disease ID:MONDO:0019332
Submitter: Orphanet
Inheritance Pattern: AD
Disease ID:MONDO:0019272
Submitter: Ambry Genetics
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to COL14A1 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_021110.4. 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 | 13 | 12 | 28 | ||
| missense | 213 | 21 | 6 | 240 | ||
| nonsense | 1 | 1 | ||||
| start loss | 0 | |||||
| frameshift | 1 | 1 | ||||
| splice donor/acceptor (+/-2bp) | 14 | 14 | ||||
| Total | 0 | 0 | 232 | 34 | 18 | 284 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_066933.1 | 47 | MANE Select | |
| Ensembl | ENSP00000297848.3 | 47 | MANE Select | |
| RefSeq | NP_001371876.1 | 47 | Standard | |
| RefSeq | NP_001400419.1 | 47 | Standard |
Model Organisms & Knockout Phenotypes
Observed phenotypic effects in mouse and zebrafish models
| Gene / Model | Organism | Observed Phenotype |
|---|---|---|
| col14a1a | Danio rerio | Structure: dermis Quality: broken abnormal |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Protein digestion and absorption - Homo sapiens (human)
- Collagen chain trimerization
- Collagen biosynthesis and modifying enzymes
- Collagen degradation
- Collagen formation
Biological Process
- growth plate cartilage chondrocyte morphogenesis
- extracellular matrix organization
- collagen fibril organization
- cell-cell adhesion
Molecular Function
- RNA binding
- extracellular matrix structural constituent
- collagen binding
- extracellular matrix structural constituent conferring tensile strength
- protein binding, bridging
Cellular Component
- extracellular region
- collagen trimer
- collagen type XIV trimer
- extracellular space
- endoplasmic reticulum lumen
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000297848
- Coding exons
- 47
- Length
- 312257
- Individuals with no LoFs
- 125649
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 99
- Defined
- 125748
- p
- 0.000394
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 1.54 | 843 | 979 | 0.861 | 0.0000513 | 11567 |
| Missense (PolyPhen) | 336 | 446.6 | 0.75236 | 5310 | ||
| Synonymous | 0.0110 | 356 | 356 | 0.999 | 0.0000203 | 3604 |
| Loss of Function | 5.47 | 42 | 102 | 0.414 | 0.00000554 | 1213 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00043 | 0.00043 | rare |
| Latino/Admixed American | 0.00033 | 0.00032 | rare |
| Ashkenazi Jewish | 0.00041 | 0.00040 | rare |
| East Asian | 0.00071 | 0.00065 | rare |
| Finnish | 0.00019 | 0.00018 | rare |
| European (Non-Finnish) | 0.00039 | 0.00038 | rare |
| South Asian | 0.00053 | 0.00052 | rare |
| Other | 0.00033 | 0.00033 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Plays an adhesive role by integrating collagen bundles. It is probably associated with the surface of interstitial collagen fibrils via COL1. The COL2 domain may then serve as a rigid arm which sticks out from the fibril and protrudes the large N-terminal globular domain into the extracellular space, where it might interact with other matrix molecules or cell surface receptors (By similarity). {ECO:0000250, ECO:0000269|PubMed:2187872}.;
Recessive Scores
- pRec
- 0.186
Intolerance Scores
- LoFtool
- 0.172
- RVIS EVS
- -1.11
- RVIS percentile EVS
- 6.72
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.699
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |