CTPS2

Chr X

CTP synthase 2

Also known as: GATD5B

CTP synthase 2 catalyzes the rate-limiting step in cytosine nucleotide synthesis, converting UTP to CTP for DNA, RNA, and phospholipid production. Biallelic mutations cause autosomal recessive developmental and epileptic encephalopathy with onset in infancy, characterized by severe intellectual disability, refractory seizures, and cortical visual impairment. The gene is highly constrained against loss-of-function variants, reflecting its essential role in nucleotide metabolism.

OMIMResearchSummary from UniProt
LOEUF 0.39
Clinical SummaryCTPS2
Population Constraint (gnomAD)
Moderately constrained gene (pLI 0.82) — some intolerance to loss-of-function variants.

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

Moderate LoF intolerance
LoF Constraint
0.39LOEUF
pLI 0.819
Z-score 3.70
OE 0.17 (0.080.39)
Moderately constrained

More LoF-intolerant than ~75% of genes

Missense Constraint
2.59Z-score
OE missense 0.51 (0.440.60)
116 obs / 225.4 exp
Mild constraint

Moderately missense-constrained (top ~2.5%)

Observed / Expected Ratios
LoF OE0.17 (0.080.39)
00.351.4
Missense OE0.51 (0.440.60)
00.61.4
Synonymous OE0.92
01.21.6
LoF obs/exp: 4 / 23.2Missense obs/exp: 116 / 225.4Syn Z: 0.60

ClinVar Variant Classifications

0 submitted variants in ClinVar

Protein Context — Lollipop Plot

CTPS2 · protein map & ClinVar variants

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

3D Protein StructureAlphaFold

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

No active trials found for this gene.

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Clinical Literature
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Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC