HOXC6

Chr 12

homeobox C6

Also known as: CP25, HHO.C8, HOX3, HOX3C

NCBI Gene: 3223ENSG00000197757UniProt: P09630

This gene belongs to the homeobox family, members of which 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, HOXC6, is one of several HOXC genes located in a cluster on chromosome 12. Three genes, HOXC5, HOXC4 and HOXC6, share a 5' non-coding exon. Transcripts may include the shared exon spliced to the gene-specific exons, or they may include only the gene-specific exons. Alternatively spliced transcript variants encoding different isoforms have been identified for HOXC6. Transcript variant two includes the shared exon, and transcript variant one includes only gene-specific exons. [provided by RefSeq, Jul 2008]

ResearchGenerating clinical summary…

Clinical highlights

Interpreting a novel variant
This gene is strongly intolerant of loss-of-function variation in the population, so LoF variants warrant close attention. No curated mechanism annotation is available — see the mechanism card for the computational prediction and its caveats.Based on population constraint only.
0
Active trials
35
Pubs (1 yr)
—
P/LP submissions
—
P/LP missense
0.60
LOEUF
Multiple*
Mechanism· predicted
Some data sources returned errors (1)

omim: Error: OMIM fetch failed: 429

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Moderate LoF intolerance
LoF Constraint?
0.60LOEUF
pLI 0.512
Z-score 2.43
OE 0.19 (0.08–0.60)
Moderately constrained

More LoF-intolerant than ~75% of genes

Missense Constraint?
0.97Z-score
OE missense 0.77 (0.66–0.90)
107 obs / 139.3 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios?
LoF OE?0.19 (0.08–0.60)
0≤0.351.4
Missense OE?0.77 (0.66–0.90)
0≤0.61.4
Synonymous OE?0.91
0≤1.21.6
LoF obs/exp: 2 / 10.5Missense obs/exp: 107 / 139.3Syn Z: 0.53

ClinVar Variant Classifications

0 submitted variants in ClinVar

ClinVar

Protein Context — Lollipop Plot

HOXC6 · 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