PSAT1

Chr 9AR

phosphoserine aminotransferase 1

Also known as: EPIP, NLS2, PSA, PSAT, PSATD

NCBI Gene: 29968ENSG00000135069UniProt: Q9Y617

This gene encodes a member of the class-V pyridoxal-phosphate-dependent aminotransferase family. The encoded protein is a phosphoserine aminotransferase and decreased expression may be associated with schizophrenia. Mutations in this gene are also associated with phosphoserine aminotransferase deficiency. Alternative splicing results in multiple transcript variants. Pseudogenes of this gene have been defined on chromosomes 1, 3, and 8. [provided by RefSeq, Jul 2013]

Primary Disease Associations & Inheritance

Neu-Laxova syndrome 2MIM #616038
AR
Phosphoserine aminotransferase deficiencyMIM #610992
AR
0
Active trials
76
Pathogenic / LP
361
ClinVar variants
62
Pubs (1 yr)
0.4
Missense Z
1.27
LOEUF
Clinical Summary— PSAT1
🧬
Gene-Disease Validity (ClinGen)
neurometabolic disorder due to serine deficiency · ARDefinitive

Definitive — sufficient evidence for diagnostic panels

⚡
Population Constraint (gnomAD)
Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.
📋
ClinVar Variants
76 Pathogenic / Likely Pathogenic· 105 VUS of 361 total submissions
📖
GeneReview available — PSAT1
Authoritative clinical overview · Recommended first read
Open GeneReview ↗

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Tolerant — LoF & missense variants common in population
LoF Constraint
1.27LOEUF
pLI 0.000
Z-score 0.71
OE 0.81 (0.54–1.27)
Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint
0.41Z-score
OE missense 0.92 (0.81–1.04)
185 obs / 201.5 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios
LoF OE0.81 (0.54–1.27)
0≤0.351.4
Missense OE0.92 (0.81–1.04)
0≤0.61.4
Synonymous OE0.93
0≤1.21.6
LoF obs/exp: 14 / 17.2Missense obs/exp: 185 / 201.5Syn Z: 0.50
DN
DN
0.6161th %ile
GOF
0.4480th %ile
LOF
0.3746th %ile

The highest-scoring mechanism for this gene is dominant-negative.

DNprediction above median

Note: In-silico variant effect predictors (SIFT, PolyPhen, REVEL, CADD) may underestimate pathogenicity of missense variants in genes with GOF or DN mechanisms. Consider functional evidence and clinical context.

Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312.

ClinVar Variant Classifications

361 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic57
Likely Pathogenic19
VUS105
Likely Benign132
Benign41
Conflicting7
57
Pathogenic
19
Likely Pathogenic
105
VUS
132
Likely Benign
41
Benign
7
Conflicting

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
9
2
46
0
57
Likely Pathogenic
8
3
8
0
19
VUS
2
89
14
0
105
Likely Benign
0
2
52
78
132
Benign
0
0
37
4
41
Conflicting
—7
Total199615782361

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

View in ClinVar →

PSAT1 · protein map & ClinVar variants

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

Gene2Phenotype Curations

PSAT1-related Neu-Laxova syndrome

strong
ARLoss Of FunctionAbsent Gene Product
Dev. Disorders
G2P ↗

Gene2Phenotype curations · DECIPHER consortium patient cohort (public variants) · deciphergenomics.org

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

Search ClinicalTrials.gov →
Clinical Literature
Landmark / reviewRecent case evidence
Full-Text Mentions
NLP-detected gene mentions in article bodies · via PubTator3
PubTator3
Top 5 full-text resultsSearch PubTator3 ↗
Key Publications
Landmark & review papers · by relevance
PubMed
Top 5 results · since 2015Search PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
Top 5 resultsSearch Europe PMC ↗

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