HCFC1R1

Chr 16

host cell factor C1 regulator 1

Also known as: HPIP

NCBI Gene: 54985 ENSG00000103145 UniProt: Q9NWW0

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.

ResearchSummary from RefSeq, UniProt

Predicted to be located in cytoplasm and nucleus. [provided by Alliance of Genome Resources, Jun 2026]

ResearchGenerating clinical summary…

Active trials

Pubs (1 yr)

—

P/LP submissions

—

P/LP missense

1.72

LOEUF

—

Mechanism

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?

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

Background carrier burden — how many people carry a rare variant somewhere in HCFC1R1?

gnomAD v4 · ~731k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 200

256 rare PASS variants

Rare truncating (LoF)

1 in 4,000

50 rare PASS variants

Rare synonymous (reference)

1 in 550

104 rare PASS variants

Truncating variants are far rarer here than missense — that gap, in human units, is what constraint means for HCFC1R1. A background rate for each class, not the frequency of any particular variant; thin-coverage exons undercount.

By genetic ancestry · 9 gnomAD groups · rare = under 0.1% in that group

Group	People	Missense	Truncating
European (non-Finnish)	~556k	1 in 310	1 in 5,900
South Asian	~43k	1 in 210	1 in 3,100
Remaining (unassigned)	~30k	1 in 150	≈ 1 in 9,500
European (Finnish)	~27k	1 in 1,700	1 in 1,200
Admixed American	~22k	1 in 210	1 in 2,000
African / African American	~21k	1 in 210	1 in 2,500
East Asian	~20k	1 in 290	1 in 1,800
Ashkenazi Jewish	~13k	1 in 2,500	≈ 1 in 13,000
Middle Eastern	~2,880	1 in 310	≈ 1 in 2,600

Each group is summed over the variants that are rare in that group. Grey ≈ figures rest on fewer than five expected carriers — too few to distinguish groups. Differences mostly reflect how many people were sampled and how much variation each ancestry carries, not disease risk.

Exome coverage (gnomAD): All 4 coding exons well covered in gnomAD exomes and genomes.? see exons ↓