HCFC1R1

Chr 16

host cell factor C1 regulator 1

Also known as: HPIP

NCBI Gene: 54985 ENSG00000103145 UniProt: Q9NWW0 OMIM: 618818

HCFC1R1 encodes a protein that regulates the transcriptional coactivator HCFC1 by controlling its subcellular localization between the nucleus and cytoplasm. Mutations in HCFC1R1 have not been definitively associated with human disease in the medical literature. This gene shows low constraint against loss-of-function variants, suggesting it may be tolerant to complete protein loss.

OMIM ResearchSummary from RefSeq, UniProt

Located in nucleoplasm. [provided by Alliance of Genome Resources, Jul 2025]

OMIM ResearchGenerating clinical summary…

LOEUF 1.72

Clinical Summary— HCFC1R1

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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

27 VUS of 37 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?

1.72LOEUF

pLI 0.001

Z-score 0.24

OE 0.89 (0.46–1.72)

Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint?

-0.53Z-score

OE missense 1.17 (0.98–1.41)

84 obs / 71.5 exp

Tolerant

Tolerant to missense variation

Observed / Expected Ratios?

LoF OE?0.89 (0.46–1.72)

0≤0.351.4

Missense OE?1.17 (0.98–1.41)

0≤0.61.4

Synonymous OE?1.09

0≤1.21.6

LoF obs/exp: 5 / 5.6Missense obs/exp: 84 / 71.5Syn Z: -0.37

ClinVar Variant Classifications

37 submitted variants in ClinVar

ClinVar

Classification Summary

VUS27

VUS

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

Classification	Missense + Inframe	Total
Pathogenic	0	0
Likely Pathogenic	0	0
VUS	27	27
Likely Benign	0	0
Benign	0	0
Total	27	27

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

View in ClinVar →

35 pathogenic / likely-pathogenic (of 44) ClinVar copy-number / structural variants overlap HCFC1R1 — these span large chromosomal regions, not the gene specifically, and are excluded from the counts above. Explore in CNV tools →