ASS1 p.Asn271=
c.813C>T · rs1361123853 · VCV1148982
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00169%, nfe)
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 1.8 | GERP -0.67, phastCons 1 |
| Overall | ||
| CADD | 10.97 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00169%
European (non-Finnish) · 20/1,180,028 alleles
Filtering AF
0.00111%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0009%
Overall
0.00137%
20/1,461,828 alleles · very rare
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.Asn271=
- Coding
- c.813C>T
- MANE Select
- NM_054012
- dbSNP
- rs1361123853
- Type
- single nucleotide variant
- Location
- chr9:130480424 (GRCh38)
- Gene constraint
- LOEUF 1.14 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 95.64 · 1 PDB
- Residue 271
- a β-strand; a UniProt-annotated variant site (in ctln1)
Similar variants
- ASS1 p.Asn271fs Pathogenic/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
- ASS1 c.496-2A>G 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/ass1-p-asn271 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown