PCYT1A

Chr 3

phosphate cytidylyltransferase 1A, choline

Also known as: CCTA, CCTalpha, CGL5, CT, CTA, CTPCT, PCYT1, SMDCRD

NCBI Gene: 5130ENSG00000161217UniProt: P49585

This gene belongs to the cytidylyltransferase family and is involved in the regulation of phosphatidylcholine biosynthesis. Mutations in this gene are associated with spondylometaphyseal dysplasia with cone-rod dystrophy. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Aug 2015]

ResearchGenerating clinical summary…

Primary Disease Associations & Inheritance

UniProtSpondylometaphyseal dysplasia with cone-rod dystrophy
UniProtLipodystrophy, congenital generalized, 5

Clinical highlights

Gene-disease validity (ClinGen)
spondylometaphyseal dysplasia-cone-rod dystrophy syndrome · 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.
4
Active trials
16
Pubs (1 yr)
—
P/LP submissions
—
P/LP missense
0.86
LOEUF
LOF
Mechanism· G2P
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?
0.86LOEUF
pLI 0.000
Z-score 2.06
OE 0.52 (0.33–0.86)
Tolerant

Typical tolerance to LoF variation

Missense Constraint?
1.64Z-score
OE missense 0.68 (0.60–0.79)
145 obs / 212.0 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios?
LoF OE?0.52 (0.33–0.86)
0≤0.351.4
Missense OE?0.68 (0.60–0.79)
0≤0.61.4
Synonymous OE?1.07
0≤1.21.6
LoF obs/exp: 11 / 21.2Missense obs/exp: 145 / 212.0Syn Z: -0.52

ClinVar Variant Classifications

0 submitted variants in ClinVar

ClinVar

Protein Context — Lollipop Plot

PCYT1A · 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