ASNS p.Thr139=
c.417A>G · rs1562820343 · VCV2179858
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00636%, nfe)
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 -0.39 | GERP -3.4, phastCons 0.01 |
| Overall | ||
| CADD | 5.038 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00636%
European (non-Finnish) · 75/1,179,782 alleles
Filtering AF
0.00519%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00474%
Overall
0.00513%
75/1,461,468 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
- ASNS
- Protein
- p.Thr139=
- Coding
- c.417A>G
- MANE Select
- NM_001673
- dbSNP
- rs1562820343
- Type
- single nucleotide variant
- Location
- chr7:97864329 (GRCh38)
- Gene constraint
- LOEUF 0.745 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 94.36 · 3 PDB
- Residue 139
- the glutamine amidotransferase type-2 domain
Similar variants
- ASNS p.Thr139Ile Uncertain significance ★ ⚠ same residue
- ASNS c.1030+1G>A Likely pathogenic ★★ same type
- ASNS c.1138-1G>A Likely pathogenic ★★ same type
- ASNS c.1239-2A>T Likely pathogenic ★★ same type
- ASNS c.1320+1G>C Likely pathogenic ★★ same type
- ASNS c.1320+1G>T Likely pathogenic ★★ same type
- ASNS c.1321-1G>A Likely pathogenic ★★ same type
- ASNS c.1476+1G>A Pathogenic ★★ same type
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/asns-p-thr139 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown