HOXC13

Chr 12

homeobox C13

Also known as: ECTD9, HOX3, HOX3G

NCBI Gene: 3229ENSG00000123364UniProt: P31276

This gene belongs to the homeobox family of genes. The homeobox genes encode a highly conserved family of transcription factors that play an important role in morphogenesis in all multicellular organisms. Mammals possess four similar homeobox gene clusters, HOXA, HOXB, HOXC and HOXD, which are located on different chromosomes and consist of 9 to 11 genes arranged in tandem. This gene is one of several homeobox HOXC genes located in a cluster on chromosome 12. The product of this gene may play a role in the development of hair, nail, and filiform papilla. [provided by RefSeq, Jul 2008]

ResearchGenerating clinical summary…

Primary Disease Associations & Inheritance

UniProtEctodermal dysplasia 9, hair/nail type

Clinical highlights

Interpreting a novel variant
Loss of function is the curated mechanism (Gene2Phenotype) and the gene is intolerant of it in the population — truncating, frameshift and canonical splice variants carry more prior weight here than missense.Curated gene-level mechanism — a prior for triage, not a per-variant call.
0
Active trials
19
Pubs (1 yr)
—
P/LP submissions
—
P/LP missense
0.66
LOEUF
LOF
Mechanism· G2P
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?
0.66LOEUF
pLI 0.420
Z-score 2.26
OE 0.21 (0.09–0.66)
Tolerant

Typical tolerance to LoF variation

Missense Constraint?
0.55Z-score
OE missense 0.88 (0.77–1.01)
142 obs / 161.7 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios?
LoF OE?0.21 (0.09–0.66)
0≤0.351.4
Missense OE?0.88 (0.77–1.01)
0≤0.61.4
Synonymous OE?0.89
0≤1.21.6
LoF obs/exp: 2 / 9.5Missense obs/exp: 142 / 161.7Syn Z: 0.74

ClinVar Variant Classifications

0 submitted variants in ClinVar

ClinVar

Protein Context — Lollipop Plot

HOXC13 · protein map & ClinVar variants

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

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

Search ClinicalTrials.gov →

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