ASS1 p.Val263=
c.789G>A · rs1419381608 · VCV763379
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0263%, sas)
Conditions
1
citrullinemia
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 1.2 | GERP 0.44, phastCons 1 |
| Overall | ||
| CADD | 9.767 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0263%
South Asian · 24/91,084 alleles
Filtering AF
0.0181%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0154%
Overall
0.00167%
27/1,614,206 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0263% | 3,795 |
| Remaining individualsnot grpmax-eligible | 0.0032% | 31,256 |
| European (non-Finnish) | 8.47e-05% | 1,180,027 |
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
- ASS1
- Protein
- p.Val263=
- Coding
- c.789G>A
- MANE Select
- NM_054012
- dbSNP
- rs1419381608
- Type
- single nucleotide variant
- Location
- chr9:130480400 (GRCh38)
- Gene constraint
- LOEUF 1.14 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 95.64 · 1 PDB
- Residue 263
- a UniProt-annotated variant site (in ctln1); a UniProt-annotated variant site (in ctln1; mild clinical course; no effect on affinity for aspartate; no effect on affinity for citrulline; decreased argininosuccinate synthase activity)
Similar variants
- ASS1 p.Val263Met Pathogenic ★★ same residue
- ASS1 p.Val263Glu Likely pathogenic ★ same residue
- ASS1 c.1194-1G>C Pathogenic/Likely pathogenic ★★ same condition
- ASS1 c.174+1G>A Pathogenic/Likely pathogenic ★★ same condition
- ASS1 c.174+1G>T Pathogenic/Likely pathogenic ★★ same condition
- ASS1 c.175-1119G>A Pathogenic/Likely pathogenic ★★ same condition
- ASS1 c.364-2A>T Likely pathogenic ★★ same condition
- ASS1 c.421-2A>G 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/ass1-p-val263 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown