ACP3

Chr 3

acid phosphatase 3

Also known as: 5'-NT, ACP-3, ACPP, TM-PAP

NCBI Gene: 55 ENSG00000014257 UniProt: P15309 OMIM: 171790

This gene encodes an enzyme that catalyzes the conversion of orthophosphoric monoester to alcohol and orthophosphate. It is synthesized under androgen regulation and is secreted by the epithelial cells of the prostate gland. An alternatively spliced transcript variant encoding a longer isoform has been found for this gene. This isoform contains a transmembrane domain and is localized in the plasma membrane-endosomal-lysosomal pathway. [provided by RefSeq, Sep 2008]

OMIM Research

OMIM ResearchGenerating clinical summary…

Active trials

Pubs (1 yr)

—

P/LP submissions

—

P/LP missense

1.40

LOEUF

Mechanism· predicted

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

1.40LOEUF

pLI 0.000

Z-score 0.01

OE 1.00 (0.72–1.40)

Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint?

0.17Z-score

OE missense 0.97 (0.87–1.08)

221 obs / 228.2 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?1.00 (0.72–1.40)

0≤0.351.4

Missense OE?0.97 (0.87–1.08)

0≤0.61.4

Synonymous OE?1.04

0≤1.21.6

LoF obs/exp: 24 / 24.1Missense obs/exp: 221 / 228.2Syn Z: -0.31

Background carrier burden — how many people carry a rare variant somewhere in ACP3?

gnomAD v4 · ~731k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 95

590 rare PASS variants

Rare truncating (LoF)

1 in 400

101 rare PASS variants

Rare synonymous (reference)

1 in 210

201 rare PASS variants

Rare missense and truncating variants are carried at similar rates in ACP3; 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 130	1 in 630
South Asian	~43k	1 in 100	1 in 330
Remaining (unassigned)	~30k	1 in 80	1 in 1,300
European (Finnish)	~27k	1 in 270	≈ 1 in 13,000
Admixed American	~22k	1 in 100	1 in 480
African / African American	~21k	1 in 96	1 in 710
East Asian	~20k	1 in 130	1 in 890
Ashkenazi Jewish	~13k	1 in 730	≈ 1 in 4,100
Middle Eastern	~2,884	1 in 85	≈ 1 in 1,400

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