PSAT1 p.Pro87=
c.261C>T · rs909218310 · VCV1654246
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.000254%, nfe)
Conditions
1
Neu-Laxova syndrome 2
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -1.5 | |
| Overall | ||
| CADD | 5.332 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000254%
European (non-Finnish) · 3/1,180,044 alleles
Filtering AF
6.8e-05%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.9e-05%
Overall
0.000186%
3/1,614,072 alleles · very rare
exomes 2/1,461,886 · genomes 1/152,186 · joint denominator
Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.
Variant & gene context
- Gene
- PSAT1
- Protein
- p.Pro87=
- Coding
- c.261C>T
- MANE Select
- NM_058179
- dbSNP
- rs909218310
- Type
- single nucleotide variant
- Location
- chr9:78304804 (GRCh38)
- Gene constraint
- LOEUF 1.305 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 97.09 · 3 PDB
- Residue 87
- a UniProt-annotated variant site (has no effect on o-phospho-l-serine:2-oxoglutarate aminotransferase catalytic efficiency; does not affect km for 3-phosphohydroxypyruvate; does not affect km for l-glutamate; no effect on function in l-serine biosynthesis shown through in vitro reconstruction of the phosphorylated pathway; does not affect secondary structure; does not affect dimerization; does not affect thermal stability); an α-helix
Similar variants
- PSAT1 p.Pro87His Uncertain significance ★ ⚠ same residue
- PSAT1 p.Pro87Leu Uncertain significance ★ ⚠ same residue
- PSAT1 c.570+2T>C Likely pathogenic ★★ same condition
- PSAT1 c.870-1G>T Pathogenic/Likely pathogenic ★★ same condition
- PSAT1 p.Arg222Ter Pathogenic/Likely pathogenic ★★ same condition
- PSAT1 p.Asp100Ala Pathogenic/Likely pathogenic ★★ same condition
- PSAT1 p.Glu280Ter Pathogenic/Likely pathogenic ★★ same condition
- PSAT1 p.Glu317Ter Pathogenic/Likely pathogenic ★★ same condition
Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →
Cite Sugi Variant
Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/psat1-p-pro87 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown