PSAT1 p.Arg45=
c.135G>A · rs372097888 · VCV1917641
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0107%, afr)
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 0.57 | phastCons 0.99 |
| Overall | ||
| CADD | 5.527 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0107%
African / African-American · 8/74,816 alleles
Filtering AF
0.00529%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00381%
Overall
0.000559%
9/1,610,300 alleles · ultra-rare
exomes 2/1,458,164 · genomes 7/152,136 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0107% | 9,352 |
| European (non-Finnish) | 8.5e-05% | 1,176,796 |
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.Arg45=
- Coding
- c.135G>A
- MANE Select
- NM_058179
- dbSNP
- rs372097888
- Type
- single nucleotide variant
- Location
- chr9:78301967 (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 45
- a binding site
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-arg45 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown