PSAT1

Chr 9AR

phosphoserine aminotransferase 1

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

This gene encodes phosphoserine aminotransferase, which catalyzes the second step of L-serine biosynthesis by converting 3-phosphohydroxypyruvate and L-glutamate to O-phosphoserine and alpha-ketoglutarate. Biallelic mutations cause phosphoserine aminotransferase deficiency and Neu-Laxova syndrome 2 with autosomal recessive inheritance. The gene is not highly constrained against loss-of-function variants, consistent with the recessive inheritance pattern of associated disorders.

GeneReviewsOMIMResearchSummary from RefSeq, OMIM, UniProt
LOFmechanismARLOEUF 1.272 OMIM phenotypes
Clinical SummaryPSAT1
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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.
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ClinVar Variants
37 unique Pathogenic / Likely Pathogenic· 91 VUS of 400 total submissions
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GeneReview available — PSAT1
Authoritative clinical overview · Recommended first read
Open GeneReview ↗

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

Tolerant — LoF & missense variants common in population
LoF Constraint
1.27LOEUF
pLI 0.000
Z-score 0.71
OE 0.81 (0.541.27)
Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint
0.41Z-score
OE missense 0.92 (0.811.04)
185 obs / 201.5 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios
LoF OE0.81 (0.541.27)
00.351.4
Missense OE0.92 (0.811.04)
00.61.4
Synonymous OE0.93
01.21.6
LoF obs/exp: 14 / 17.2Missense obs/exp: 185 / 201.5Syn Z: 0.50
Curated Mechanism (G2P)Gene2Phenotype (DDG2P) ↗
strongPSAT1-related Neu-Laxova syndromeLOFAR

Predictions shown for reference only — model trained on dominant genes, not applicable to AR conditions.

DN
0.6161th %ile
GOF
0.4480th %ile
LOF
0.3746th %ile

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

400 submitted variants in ClinVar

Classification Summary

Pathogenic23
Likely Pathogenic14
VUS91
Likely Benign126
Benign32
Conflicting3
23
Pathogenic
14
Likely Pathogenic
91
VUS
126
Likely Benign
32
Benign
3
Conflicting

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
13
0
10
0
23
Likely Pathogenic
11
2
1
0
14
VUS
1
81
9
0
91
Likely Benign
0
0
49
77
126
Benign
0
0
32
0
32
Conflicting
3
Total258310177289

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

View in ClinVar →

Protein Context — Lollipop Plot

PSAT1 · 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.

Search ClinicalTrials.gov →
Clinical Literature
Open Research Assistant →