PSAT1 p.Arg342=
c.1026G>A · rs769706393 · VCV2897815
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.000424%, 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 -0.3 | GERP -1.8, phastCons 0.05 |
| Overall | ||
| CADD | 6.293 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000424%
European (non-Finnish) · 5/1,179,802 alleles
Filtering AF
0.000124%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 9e-05%
Overall
0.00031%
5/1,613,790 alleles · very rare
exomes 5/1,461,542 · genomes 0/152,248 · 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.Arg342=
- Coding
- c.1026G>A
- MANE Select
- NM_058179
- dbSNP
- rs769706393
- Type
- single nucleotide variant
- Location
- chr9:78328999 (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 342
- a binding site; a UniProt-annotated variant site (in nls2; loss of o-phospho-l-serine:2-oxoglutarate aminotransferase activity; loss of function in l-serine biosynthesis shown through in vitro reconstruction of the phosphorylated pathway); a β-strand
Similar variants
- PSAT1 p.Arg342Gln Uncertain significance ★ ⚠ same residue
- PSAT1 p.Arg342Trp Uncertain significance ★ ⚠ same residue
- PSAT1 p.Arg342fs Pathogenic 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
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-arg342 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown