COL13A1

Chr 10

collagen type XIII alpha 1 chain

Also known as: CMS19, COLXIIIA1

NCBI Gene: 1305ENSG00000197467UniProt: Q5TAT6

This gene encodes the alpha chain of one of the nonfibrillar collagens. The function of this gene product is not known, however, it has been detected at low levels in all connective tissue-producing cells so it may serve a general function in connective tissues. Unlike most of the collagens, which are secreted into the extracellular matrix, collagen XIII contains a transmembrane domain and the protein has been localized to the plasma membrane. The transcripts for this gene undergo complex and extensive splicing involving at least eight exons. Like other collagens, collagen XIII is a trimer; it is not known whether this trimer is composed of one or more than one alpha chain isomer. A number of alternatively spliced transcript variants have been described, but the full length nature of some of them has not been determined. [provided by RefSeq, Jul 2008]

GeneReviewsResearchGenerating clinical summary…

Primary Disease Associations & Inheritance

UniProtMyasthenic syndrome, congenital, 19

Clinical highlights

Interpreting a novel variant
Loss of function is the curated mechanism (Gene2Phenotype), though the gene is not strongly LoF-constrained in the population — weigh truncating variants against that tolerance.Curated gene-level mechanism — a prior for triage, not a per-variant call.
1
Active trials
25
Pubs (1 yr)
—
P/LP submissions
—
P/LP missense
0.75
LOEUF
LOF
Mechanism· G2P
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GeneReview available — COL13A1
Authoritative clinical overview · Recommended first read
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Some data sources returned errors (1)

omim: Error: OMIM fetch failed: 429

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Tolerant — LoF & missense variants common in population
LoF Constraint?
0.75LOEUF
pLI 0.000
Z-score 3.05
OE 0.56 (0.42–0.75)
Tolerant

Typical tolerance to LoF variation

Missense Constraint?
0.77Z-score
OE missense 0.89 (0.82–0.97)
364 obs / 407.8 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios?
LoF OE?0.56 (0.42–0.75)
0≤0.351.4
Missense OE?0.89 (0.82–0.97)
0≤0.61.4
Synonymous OE?1.13
0≤1.21.6
LoF obs/exp: 31 / 55.6Missense obs/exp: 364 / 407.8Syn Z: -1.23

ClinVar Variant Classifications

0 submitted variants in ClinVar

ClinVar

Protein Context — Lollipop Plot

COL13A1 · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

External Resources

Links to major genomics databases and tools

Franklin by Genoox
AI-powered variant curation and clinical analysis
DECIPHER
Genomic variants and phenotypes in rare disease patients