ASTN2 p.Pro820=
c.2460G>C · rs143522238 · VCV3040520
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0746%, afr)
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 -3.2 | GERP -3.9 |
| Overall | ||
| CADD | 6.19 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0746%
African / African-American · 56/75,022 alleles
Filtering AF
0.059%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0533%
Overall
0.00403%
65/1,614,130 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0746% | 1,340 |
| Remaining individualsnot grpmax-eligible | 0.008% | 12,502 |
| Admixed American | 0.00333% | 30,010 |
| European (non-Finnish) | 0.000169% | 590,012 |
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.Pro820=
- Coding
- c.2460G>C
- MANE Select
- NM_001365068
- dbSNP
- rs143522238
- Type
- single nucleotide variant
- Location
- chr9:116733460 (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
- ASTN2 p.Pro820Leu Uncertain significance ★ ⚠ same residue
- 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
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-pro820 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown