ASTN2 p.Pro604=
c.1812G>A · rs773572727 · VCV3039475
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00223%, eas)
Conditions
1
ASTN2-related disorder
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 -8.5 | GERP -3.9 |
| Overall | ||
| CADD | 2.011 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00223%
East Asian · 1/44,826 alleles
Filtering AF
0.000615%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000474%
Overall
0.000992%
16/1,613,338 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.00223% | 44,826 |
| Admixed American | 0.00167% | 59,950 |
| European (non-Finnish) | 0.0011% | 90,746 |
| South Asian | 0.0011% | 90,936 |
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
- ASTN2
- Protein
- p.Pro604=
- Coding
- c.1812G>A
- MANE Select
- NM_001365068
- dbSNP
- rs773572727
- Type
- single nucleotide variant
- Location
- chr9:116975285 (GRCh38)
- Gene constraint
- LOEUF 0.473 · pLI 0.99 · ClinGen HI 1/3 (gnomAD)
- Structure
- AlphaFold pLDDT 64.93 · 3 PDB
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-pro604 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown