C3ORF52

Chr 3AR

chromosome 3 open reading frame 52

Also known as: HYPT15, TTMP

NCBI Gene: 79669 ENSG00000114529 UniProt: Q5BVD1 OMIM: 611956

This protein facilitates LIPH-mediated synthesis of 2-acyl lysophosphatidic acid (LPA), a bioactive lipid mediator necessary for hair formation and growth. Mutations cause hypotrichosis 15, an autosomal recessive condition characterized by sparse hair development. The gene shows low constraint to loss-of-function variation (pLI 0.00009, LOEUF 1.8), consistent with recessive inheritance where heterozygous carriers are typically unaffected.

OMIM ResearchSummary from RefSeq, OMIM, UniProt

Located in plasma membrane. Implicated in hypotrichosis 15. [provided by Alliance of Genome Resources, Jul 2025]

OMIM ResearchGenerating clinical summary…

ARLOEUF 1.791 OMIM phenotype

Clinical Summary— C3ORF52

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Population Constraint (gnomAD)

Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.

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ClinVar Variants

4 unique Pathogenic / Likely Pathogenic· 31 VUS of 57 total submissions

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Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

1.79LOEUF

pLI 0.000

Z-score -0.06

OE 1.03 (0.55–1.79)

Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint?

0.86Z-score

OE missense 0.78 (0.66–0.93)

97 obs / 123.8 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?1.03 (0.55–1.79)

0≤0.351.4

Missense OE?0.78 (0.66–0.93)

0≤0.61.4

Synonymous OE?0.75

0≤1.21.6

LoF obs/exp: 6 / 5.9Missense obs/exp: 97 / 123.8Syn Z: 1.41

ClinVar Variant Classifications

57 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic4

VUS31

Likely Benign5

Pathogenic

VUS

Likely Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

Classification	LoF	Missense + Inframe	Total
Pathogenic	4	0	4
Likely Pathogenic	0	0	0
VUS	2	29	31
Likely Benign	0	5	5
Benign	0	0	0
Total	6	34	40

LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly

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16 pathogenic / likely-pathogenic (of 17) ClinVar copy-number / structural variants overlap C3ORF52 — these span large chromosomal regions, not the gene specifically, and are excluded from the counts above. Explore in CNV tools →