PPP1R2

Chr 3

protein phosphatase 1 regulatory inhibitor subunit 2

Also known as: IPP-2, IPP2, PPP1R2A

NCBI Gene: 5504 ENSG00000184203 UniProt: P41236 OMIM: 601792

Protein phosphatase-1 (PP1) is one of the main eukaryotic serine/threonine phosphatases. The protein encoded by this gene binds to the catalytic subunit of PP1, strongly inhibiting its activity. Ten related pseudogenes have been found throughout the human genome. Several splice variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 2015]

OMIM Research

OMIM 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

0.75

LOEUF

Mechanism· predicted

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

0.75LOEUF

pLI 0.069

Z-score 2.19

OE 0.33 (0.16–0.75)

Tolerant

Typical tolerance to LoF variation

Missense Constraint?

0.68Z-score

OE missense 0.82 (0.69–0.97)

89 obs / 109.1 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?0.33 (0.16–0.75)

0≤0.351.4

Missense OE?0.82 (0.69–0.97)

0≤0.61.4

Synonymous OE?0.95

0≤1.21.6

LoF obs/exp: 4 / 12.3Missense obs/exp: 89 / 109.1Syn Z: 0.26

Background carrier burden — how many people carry a rare variant somewhere in PPP1R2?

gnomAD v4 · ~731k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 160

216 rare PASS variants

Rare truncating (LoF)

1 in 5,300

28 rare PASS variants

Rare synonymous (reference)

1 in 270

82 rare PASS variants

Truncating variants are far rarer here than missense — that gap, in human units, is what constraint means for PPP1R2. 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 360	1 in 7,700
South Asian	~43k	1 in 190	1 in 7,400
Remaining (unassigned)	~30k	1 in 210	≈ 1 in 7,500
European (Finnish)	~27k	1 in 3,300	1 in 5,300
Admixed American	~22k	1 in 210	none seen
African / African American	~21k	1 in 270	≈ 1 in 9,200
East Asian	~20k	1 in 780	1 in 1,300
Ashkenazi Jewish	~13k	≈ 1 in 6,500	1 in 1,000
Middle Eastern	~2,884	1 in 200	≈ 1 in 2,900

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