ASTN2 p.Ser403Ter
c.1208C>G · rs767775629 · VCV2631131
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
Consequence
nonsense (stop-gain)
predicted LoF
gnomAD v4.1
Absent
absent from gnomAD v4.1
Conditions
1
ASTN2-related disorder
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Consequence | nonsense (stop-gain) | predicted loss-of-function in a LoF-intolerant gene |
|---|---|---|
| NMD | predicted | premature termination codon in exon 5 of 23 |
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 12 | GERP 2.4, phastCons 1 |
| Overall | ||
| CADD | 40.0 | PHRED · no single calibrated threshold — expert panels disagree |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- ASTN2
- Protein
- p.Ser403Ter
- Coding
- c.1208C>G
- MANE Select
- NM_001365068
- dbSNP
- rs767775629
- Type
- single nucleotide variant
- Location
- chr9:117096112 (GRCh38)
- Gene constraint
- LOEUF 0.473 · pLI 0.99 · ClinGen HI 1/3 (gnomAD)
- Structure
- AlphaFold pLDDT 64.93 · 3 PDB
- Residue 403
- the 'disordered' region
Disease context
ASTN2-related disorder
Similar variants
- TRIM32 p.Arg500Ter Pathogenic/Likely pathogenic ★★ same condition
- TRIM32 p.Asp487Asn Pathogenic ★★ same condition
- TRIM32 p.Tyr226Ter Pathogenic/Likely pathogenic ★★ same condition
- ASTN2 p.Val880Gly Uncertain significance ★★ ⚠ same condition
- TRIM32 p.Arg147Gln Uncertain significance ★★ ⚠ same condition
- TRIM32 p.Arg238Leu Uncertain significance ★★ ⚠ same condition
- TRIM32 p.Arg563Cys Uncertain significance ★★ ⚠ same condition
- TRIM32 p.Arg596Leu 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/astn2-p-ser403ter (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown