ANP32A

Chr 15

acidic nuclear phosphoprotein 32 family member A

Also known as: C15orf1, HPPCn, I1PP2A, LANP, MAPM, PHAP1, PHAPI, PP32

NCBI Gene: 8125 ENSG00000140350 UniProt: P39687

Enables RNA binding activity. Involved in nucleocytoplasmic transport. Located in several cellular components, including endoplasmic reticulum; nucleoplasm; and perinuclear region of cytoplasm. [provided by Alliance of Genome Resources, Jun 2026]

Research

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.

Active trials

Pubs (1 yr)

—

P/LP submissions

—

P/LP missense

0.22

LOEUF· LoF intol.

LOF

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

LoF intolerant — likely haploinsufficient

LoF Constraint?

0.22LOEUF

pLI 0.990

Z-score 3.43

OE 0.00 (0.00–0.22)

Highly constrained

Highly LoF-intolerant (top ~10% of genes)

Missense Constraint?

2.53Z-score

OE missense 0.39 (0.32–0.49)

54 obs / 137.4 exp

Mild constraint

Moderately missense-constrained (top ~2.5%)

Observed / Expected Ratios?

LoF OE?0.00 (0.00–0.22)

0≤0.351.4

Missense OE?0.39 (0.32–0.49)

0≤0.61.4

Synonymous OE?0.99

0≤1.21.6

LoF obs/exp: 0 / 13.7Missense obs/exp: 54 / 137.4Syn Z: 0.04

Background carrier burden — how many people carry a rare variant somewhere in ANP32A?

gnomAD v4 · ~731k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 950

165 rare PASS variants

Rare truncating (LoF)

1 in 2,900

7 rare PASS variants

Rare synonymous (reference)

1 in 380

120 rare PASS variants

Rare missense and truncating variants are carried at similar rates in ANP32A; 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 · 9 gnomAD groups · rare = under 0.1% in that group

Group	People	Missense	Truncating
European (non-Finnish)	~556k	1 in 1,200	1 in 20,000
South Asian	~43k	1 in 560	none seen
Remaining (unassigned)	~30k	1 in 1,300	1 in 2,000
European (Finnish)	~27k	1 in 2,700	none seen
Admixed American	~22k	1 in 2,000	≈ 1 in 11,000
African / African American	~21k	1 in 820	none seen
East Asian	~20k	1 in 630	none seen
Ashkenazi Jewish	~13k	1 in 980	none seen
Middle Eastern	~2,884	1 in 410	none seen

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 7 coding exons well covered in gnomAD exomes and genomes.? see exons ↓