PTPRM

Chr 18

protein tyrosine phosphatase receptor type M

Also known as: PTPRL1, R-PTP-MU, RPTPM, RPTPU, hR-PTPu

NCBI Gene: 5797ENSG00000173482UniProt: P28827

The protein is a receptor-type protein tyrosine phosphatase that mediates cell-cell adhesion and regulates glucose transporter trafficking through dephosphorylation of p120 catenin. Mutations cause neurodevelopmental disorders with intellectual disability and seizures, inherited in an autosomal dominant pattern. This gene is highly constrained against loss-of-function variants, indicating intolerance to protein-disrupting mutations.

Summary from RefSeq, UniProt
Research Assistant →
0
Active trials
8
Pubs (1 yr)
113
P/LP submissions
0%
P/LP missense
0.23
LOEUF· LoF intol.
—
Mechanism
Clinical Summary— PTPRM
⚡
Population Constraint (gnomAD)
Highly constrained gene — heterozygous loss-of-function variants are very rare in the population (pLI 1.00). One damaged copy is likely sufficient to cause disease.
📋
ClinVar Variants
108 unique Pathogenic / Likely Pathogenic· 191 VUS of 381 total submissions
Explore recent and relevant literature in Research Assistant →

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
LoF intolerant — likely haploinsufficient
LoF Constraint
0.23LOEUF
pLI 1.000
Z-score 7.25
OE 0.14 (0.09–0.23)
Highly constrained

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

Missense Constraint
2.84Z-score
OE missense 0.73 (0.68–0.78)
616 obs / 849.2 exp
Mild constraint

Moderately missense-constrained (top ~2.5%)

Observed / Expected Ratios
LoF OE0.14 (0.09–0.23)
0≤0.351.4
Missense OE0.73 (0.68–0.78)
0≤0.61.4
Synonymous OE1.04
0≤1.21.6
LoF obs/exp: 12 / 83.4Missense obs/exp: 616 / 849.2Syn Z: -0.57

ClinVar Variant Classifications

381 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic105
Likely Pathogenic3
VUS191
Likely Benign23
Benign19
Conflicting2
105
Pathogenic
3
Likely Pathogenic
191
VUS
23
Likely Benign
19
Benign
2
Conflicting

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
0
105
0
105
Likely Pathogenic
0
0
3
0
3
VUS
0
157
34
0
191
Likely Benign
0
2
8
13
23
Benign
0
1
4
14
19
Conflicting
—2
Total016015427343

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

View in ClinVar →

Protein Context — Lollipop Plot

PTPRM · 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 4 full-text resultsSearch PubTator3 ↗
Key Publications
Landmark & review papers · by relevance
PubMed
Top 5 results · since 2015Search PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
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