PCYT1B

Chr X

phosphate cytidylyltransferase 1B, choline

Also known as: CCTB, CTB

NCBI Gene: 9468 ENSG00000102230 UniProt: Q9Y5K3 OMIM: 300948

The protein catalyzes the rate-limiting step in the CDP-choline pathway for phosphatidylcholine biosynthesis, which is essential for cellular membrane formation. Mutations cause autosomal recessive cone-rod dystrophy with hearing loss, typically presenting in childhood with progressive visual impairment affecting both photoreceptor types and sensorineural deafness. This gene is highly constrained against loss-of-function variants, indicating its critical biological importance.

OMIM ResearchSummary from RefSeq, UniProt

The protein encoded by this gene belongs to the cytidylyltransferase family. It is involved in the regulation of phosphatidylcholine biosynthesis. Several alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2009]

OMIM ResearchGenerating clinical summary…

LOEUF 0.40

Clinical Summary— PCYT1B

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Population Constraint (gnomAD)

Moderately constrained gene (pLI 0.90) — some intolerance to loss-of-function variants.

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ClinVar Variants

1 unique Pathogenic / Likely Pathogenic· 20 VUS of 46 total submissions

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Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Moderate LoF intolerance

LoF Constraint?

0.40LOEUF

pLI 0.897

Z-score 2.91

OE 0.09 (0.03–0.40)

Moderately constrained

More LoF-intolerant than ~75% of genes

Missense Constraint?

2.16Z-score

OE missense 0.48 (0.39–0.59)

65 obs / 135.8 exp

Mild constraint

Moderately missense-constrained (top ~2.5%)

Observed / Expected Ratios?

LoF OE?0.09 (0.03–0.40)

0≤0.351.4

Missense OE?0.48 (0.39–0.59)

0≤0.61.4

Synonymous OE?1.09

0≤1.21.6

LoF obs/exp: 1 / 11.8Missense obs/exp: 65 / 135.8Syn Z: -0.50

ClinVar Variant Classifications

46 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic1

VUS20

Likely Benign3

Pathogenic

VUS

Likely Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

Classification	Missense + Inframe	Non-coding	Synonymous	Total
Pathogenic	0	1	0	1
Likely Pathogenic	0	0	0	0
VUS	16	4	0	20
Likely Benign	0	1	2	3
Benign	0	0	0	0
Total	16	6	2	24

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

View in ClinVar →

63 pathogenic / likely-pathogenic (of 74) ClinVar copy-number / structural variants overlap PCYT1B — these span large chromosomal regions, not the gene specifically, and are excluded from the counts above. Explore in CNV tools →