PSAT1 p.Val232=
c.696G>A · rs140331840 · VCV712336
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
rare (popmax 0.291%, afr)
Conditions
1
Neu-Laxova syndrome 2
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.65 | donor gain · deltas |
|---|---|---|
| Pangolin | Δ0.60 | gain · loss 0.24 · agrees with SpliceAI · independent |
| Constraint at this position | ||
| Conservation | phyloP 0.23 | GERP -1.6, phastCons 0.95 |
| Overall | ||
| CADD | 17.04 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.291%
African / African-American · 218/75,002 alleles
Filtering AF
0.259%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.247%
Overall
0.0147%
238/1,614,056 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.291% | 344 |
| Remaining individualsnot grpmax-eligible | 0.0192% | 5,208 |
| Admixed American | 0.01% | 10,000 |
| European (non-Finnish) | 0.000169% | 590,005 |
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.Val232=
- Coding
- c.696G>A
- MANE Select
- NM_058179
- dbSNP
- rs140331840
- Type
- single nucleotide variant
- Location
- chr9:78308539 (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 232
- an α-helix
Similar variants
- 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
- PSAT1 p.Ala112Val Uncertain significance ★★ ⚠ same condition
- PSAT1 p.Ala265Thr Uncertain significance ★★ ⚠ 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-val232 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown