PCMT1

Chr 6

protein-L-isoaspartate (D-aspartate) O-methyltransferase

Also known as: PIMT

NCBI Gene: 5110ENSG00000120265UniProt: P22061

This gene encodes a member of the type II class of protein carboxyl methyltransferase enzymes. The encoded enzyme plays a role in protein repair by recognizing and converting D-aspartyl and L-isoaspartyl residues resulting from spontaneous deamidation back to the normal L-aspartyl form. The encoded protein may play a protective role in the pathogenesis of Alzheimer's disease, and single nucleotide polymorphisms in this gene have been associated with spina bifida and premature ovarian failure. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Oct 2011]

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.
0
Active trials
20
Pubs (1 yr)
—
P/LP submissions
—
P/LP missense
0.46
LOEUF
—
Mechanism
Some data sources returned errors (1)

omim: Error: OMIM fetch failed: 429

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Moderate LoF intolerance
LoF Constraint?
0.46LOEUF
pLI 0.785
Z-score 2.95
OE 0.14 (0.06–0.46)
Moderately constrained

More LoF-intolerant than ~75% of genes

Missense Constraint?
1.90Z-score
OE missense 0.58 (0.48–0.69)
91 obs / 158.1 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios?
LoF OE?0.14 (0.06–0.46)
0≤0.351.4
Missense OE?0.58 (0.48–0.69)
0≤0.61.4
Synonymous OE?1.00
0≤1.21.6
LoF obs/exp: 2 / 13.8Missense obs/exp: 91 / 158.1Syn Z: -0.02

ClinVar Variant Classifications

0 submitted variants in ClinVar

ClinVar

Protein Context — Lollipop Plot

PCMT1 · protein map & ClinVar variants

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

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

Search ClinicalTrials.gov →

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