PP2D1

Chr 3

protein phosphatase 2C like domain containing 1

Also known as: C3orf48

NCBI Gene: 151649ENSG00000183977UniProt: A8MPX8OMIM: 621037

The protein functions as a serine/threonine phosphatase that negatively regulates MAPK signaling pathways in the cytoplasm and nucleus. This gene is highly constrained against loss-of-function variants (pLI ~0, LOEUF 1.12), suggesting that mutations would likely cause severe developmental disorders, though specific associated diseases have not yet been definitively established in the literature.

OMIMResearchSummary from RefSeq
DNmechanismLOEUF 1.12
Clinical Summary— PP2D1
⚡
Population Constraint (gnomAD)
Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.
📋
ClinVar Variants
23 unique Pathogenic / Likely Pathogenic· 5 VUS of 33 total submissions
Explore recent and relevant literature in Research Assistant →

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Tolerant — LoF & missense variants common in population
LoF Constraint
1.12LOEUF
pLI 0.000
Z-score 1.24
OE 0.64 (0.39–1.12)
Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint
1.13Z-score
OE missense 0.81 (0.73–0.91)
236 obs / 289.9 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios
LoF OE0.64 (0.39–1.12)
0≤0.351.4
Missense OE0.81 (0.73–0.91)
0≤0.61.4
Synonymous OE0.85
0≤1.21.6
LoF obs/exp: 9 / 14.0Missense obs/exp: 236 / 289.9Syn Z: 1.23
DN
0.6745th %ile
GOF
0.5562th %ile
LOF
0.3843th %ile

The highest-scoring mechanism for this gene is dominant-negative.

DNprediction above median

Note: In-silico variant effect predictors (SIFT, PolyPhen, REVEL, CADD) may underestimate pathogenicity of missense variants in genes with GOF or DN mechanisms. Consider functional evidence and clinical context.

Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312.

ClinVar Variant Classifications

33 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic23
VUS5
Likely Benign1
Benign2
23
Pathogenic
5
VUS
1
Likely Benign
2
Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
0
23
0
23
Likely Pathogenic
0
0
0
0
0
VUS
0
2
3
0
5
Likely Benign
0
0
0
1
1
Benign
0
0
1
1
2
Total0227231

LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly

View in ClinVar →

Protein Context — Lollipop Plot

PP2D1 · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

3D Protein StructureAlphaFold

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

Search ClinicalTrials.gov →
Clinical Literature
Open Research Assistant →
Full-Text Mentions
NLP-detected gene mentions in article bodies · via PubTator3
PubTator3
Top 5 full-text resultsSearch PubTator3 ↗
Key Publications
Landmark & review papers · by relevance
PubMed
Top 1 results · since 2015Search PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC

No open access results found

Top 5 resultsSearch Europe PMC ↗

External Resources

Links to major genomics databases and tools

Franklin by Genoox
AI-powered variant curation and clinical analysis
DECIPHER
Genomic variants and phenotypes in rare disease patients