APRG1

Chr 3

APRG1 tumor suppressor candidate

Also known as: C3orf35

NCBI Gene: 339883 ENSG00000198590 UniProt: Q8IVJ8 OMIM: 611429

The APRG1 protein is predicted to be located in cellular membranes, though its specific function remains unclear. Mutations in this gene have not been definitively associated with any recognized human genetic diseases. This gene appears to tolerate loss-of-function variants well based on population genetics data.

OMIM ResearchSummary from RefSeq

Predicted to be located in membrane. [provided by Alliance of Genome Resources, Jul 2025]

OMIM ResearchGenerating clinical summary…

Active trials

Pubs (1 yr)

—

P/LP submissions

—

P/LP missense

1.68

LOEUF

Multiple*

Mechanism· predicted

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

1.68LOEUF

pLI 0.049

Z-score 0.64

OE 0.62 (0.25–1.68)

Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint?

0.11Z-score

OE missense 0.97 (0.81–1.16)

89 obs / 91.9 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?0.62 (0.25–1.68)

0≤0.351.4

Missense OE?0.97 (0.81–1.16)

0≤0.61.4

Synonymous OE?0.93

0≤1.21.6

LoF obs/exp: 2 / 3.2Missense obs/exp: 89 / 91.9Syn Z: 0.32

Background carrier burden — how many people carry a rare variant somewhere in APRG1?

gnomAD v4 · ~607k individuals · PASS only

Rare means allele frequency under

Rare missense

none observed

0 rare PASS variants

Rare truncating (LoF)

1 in 2,900

13 rare PASS variants

Rare synonymous (reference)

none observed

0 rare PASS variants

Rare missense and truncating variants are carried at similar rates in APRG1; this gene does not show strong loss-of-function constraint by this measure. A background rate for each class, not the frequency of any particular variant; thin-coverage exons undercount.

By genetic ancestry · 6 gnomAD groups · rare = under 0.1% in that group

Group	People	Missense	Truncating
European (non-Finnish)	~476k	none seen	1 in 4,100
South Asian	~41k	none seen	1 in 2,000
Remaining (unassigned)	~22k	none seen	≈ 1 in 11,000
Admixed American	~19k	none seen	1 in 410
Ashkenazi Jewish	~8,423	none seen	1 in 580
East Asian	~8,364	none seen	1 in 1,100

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.