PPT1

Chr 1

palmitoyl-protein thioesterase 1

Also known as: CLN1, INCL, PPT

NCBI Gene: 5538ENSG00000131238UniProt: P50897

The protein encoded by this gene is a small glycoprotein involved in the catabolism of lipid-modified proteins during lysosomal degradation. The encoded enzyme removes thioester-linked fatty acyl groups such as palmitate from cysteine residues. Defects in this gene are a cause of infantile neuronal ceroid lipofuscinosis 1 (CLN1, or INCL) and neuronal ceroid lipofuscinosis 4 (CLN4). Two transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, Dec 2008]

GeneReviewsResearchGenerating clinical summary…

Primary Disease Associations & Inheritance

UniProtCeroid lipofuscinosis, neuronal, 1

Clinical highlights

Gene-disease validity (ClinGen)
neuronal ceroid lipofuscinosis · ARDefinitivesufficient evidence for diagnostic panels
Interpreting a novel variant
Loss of function is the curated mechanism (Gene2Phenotype), though the gene is not strongly LoF-constrained in the population — weigh truncating variants against that tolerance.Curated gene-level mechanism — a prior for triage, not a per-variant call.
1
Active trials
60
Pubs (1 yr)
—
P/LP submissions
—
P/LP missense
0.89
LOEUF
LOF
Mechanism· G2P
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GeneReview available — PPT1
Authoritative clinical overview · Recommended first read
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Some data sources returned errors (1)

omim: Error: OMIM fetch failed: 429

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Tolerant — LoF & missense variants common in population
LoF Constraint?
0.89LOEUF
pLI 0.000
Z-score 1.94
OE 0.52 (0.32–0.89)
Tolerant

Typical tolerance to LoF variation

Missense Constraint?
0.03Z-score
OE missense 0.99 (0.87–1.13)
163 obs / 164.2 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios?
LoF OE?0.52 (0.32–0.89)
0≤0.351.4
Missense OE?0.99 (0.87–1.13)
0≤0.61.4
Synonymous OE?1.18
0≤1.21.6
LoF obs/exp: 10 / 19.2Missense obs/exp: 163 / 164.2Syn Z: -1.10

ClinVar Variant Classifications

0 submitted variants in ClinVar

ClinVar

Protein Context — Lollipop Plot

PPT1 · protein map & ClinVar variants

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

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