PCYT1A
Chr 3ARphosphate cytidylyltransferase 1A, choline
Also known as: CCTA, CCTalpha, CGL5, CT, CTA, CTPCT, PCYT1, SMDCRD
The protein catalyzes the rate-limiting step in the CDP-choline pathway for phosphatidylcholine biosynthesis. Biallelic mutations cause autosomal recessive spondylometaphyseal dysplasia with cone-rod dystrophy and congenital generalized lipodystrophy type 5. Disease likely results from loss of function given the autosomal recessive inheritance pattern.
Primary Disease Associations & Inheritance
Definitive — sufficient evidence for diagnostic panels
Population Genetics & Constraint
gnomAD v4 — loss-of-function & missense intolerance
Typical tolerance to LoF variation
Mild missense constraint
Predictions shown for reference only — model trained on dominant genes, not applicable to AR conditions.
The Badonyi & Marsh prediction model was trained exclusively on dominant disease genes. Predictions are not reliable for genes with autosomal recessive inheritance and are shown at reduced opacity for reference only.
Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312.
ClinVar Variant Classifications
432 submitted variants in ClinVar
Classification Summary
Curated Variants Distribution
Classified variants from ClinVar · 5 ACMG categories
| Classification | LoF | Missense + Inframe | Non-coding | Synonymous | Total |
|---|---|---|---|---|---|
Pathogenic | 0 | 5 | 86 | 0 | 91 |
Likely Pathogenic | 3 | 4 | 2 | 0 | 9 |
VUS | 8 | 116 | 35 | 3 | 162 |
Likely Benign | 0 | 11 | 42 | 79 | 132 |
Benign | 0 | 2 | 10 | 4 | 16 |
Conflicting | — | 8 | |||
| Total | 11 | 138 | 175 | 86 | 418 |
LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly
View in 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
Clinical Trials
Active and recruiting trials from ClinicalTrials.gov
ClinSeq: A Large-Scale Medical Sequencing Clinical Research Pilot Study
ACTIVE NOT RECRUITINGThe LD Lync Study - Natural History Study of Lipodystrophy Syndromes
RECRUITINGGene Expression Profiles in Spinal Tuberculosis.
RECRUITINGExternal Resources
Links to major genomics databases and tools