PPP1R3B

Chr 8

protein phosphatase 1 regulatory subunit 3B

Also known as: GL, PPP1R4, PTG

NCBI Gene: 79660 ENSG00000173281 UniProt: Q86XI6 OMIM: 610541

The protein acts as a glycogen-targeting subunit for protein phosphatase 1, facilitating its interaction with glycogen metabolism enzymes and regulating glycogen synthesis by enhancing glycogen synthase activation while limiting glycogen breakdown. Mutations cause autosomal recessive glycogen storage disease with severe hepatomegaly, hypoglycemia, and growth retardation typically presenting in infancy. The gene is not highly constrained against loss-of-function variants, consistent with the recessive inheritance pattern observed in affected patients.

OMIM ResearchSummary from RefSeq, UniProt

This gene encodes the catalytic subunit of the serine/theonine phosphatase, protein phosphatase-1. The encoded protein is expressed in liver and skeletal muscle tissue and may be involved in regulating glycogen synthesis in these tissues. This gene may be a involved in type 2 diabetes and maturity-onset diabetes of the young. Alternate splicing results in multiple transcript variants that encode the same protein.[provided by RefSeq, Jan 2011]

OMIM ResearchGenerating clinical summary…

Active trials

Pubs (1 yr)

—

P/LP submissions

—

P/LP missense

0.99

LOEUF

Mechanism· predicted

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

0.99LOEUF

pLI 0.065

Z-score 1.60

OE 0.38 (0.17–0.99)

Tolerant

Typical tolerance to LoF variation

Missense Constraint?

-1.11Z-score

OE missense 1.25 (1.11–1.40)

198 obs / 158.7 exp

Tolerant

Tolerant to missense variation

Observed / Expected Ratios?

LoF OE?0.38 (0.17–0.99)

0≤0.351.4

Missense OE?1.25 (1.11–1.40)

0≤0.61.4

Synonymous OE?1.14

0≤1.21.6

LoF obs/exp: 3 / 7.8Missense obs/exp: 198 / 158.7Syn Z: -0.87

Background carrier burden — how many people carry a rare variant somewhere in PPP1R3B?

gnomAD v4 · ~731k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 170

483 rare PASS variants

Rare truncating (LoF)

1 in 3,200

44 rare PASS variants

Rare synonymous (reference)

1 in 260

178 rare PASS variants

Truncating variants are far rarer here than missense — that gap, in human units, is what constraint means for PPP1R3B. 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 280	1 in 3,900
South Asian	~43k	1 in 77	1 in 7,200
Remaining (unassigned)	~30k	1 in 120	1 in 1,800
European (Finnish)	~27k	1 in 550	none seen
Admixed American	~22k	1 in 150	1 in 3,700
African / African American	~21k	1 in 140	≈ 1 in 4,200
East Asian	~20k	1 in 120	1 in 2,600
Ashkenazi Jewish	~13k	≈ 1 in 6,500	≈ 1 in 13,000
Middle Eastern	~2,884	1 in 63	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 1 coding exons well covered in gnomAD exomes and genomes.? see exons ↓