ASTN2 p.Asp671=
c.2013C>T · rs113540918 · VCV3039967
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.132%, mid)
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 1.2 | GERP -2.8, phastCons 1 |
| Overall | ||
| CADD | 6.725 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.132%
Middle Eastern · 8/6,062 alleles
Filtering AF
0.0656%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0478%
Overall
0.00533%
86/1,614,148 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.132% | 758 |
| African / African-American | 0.0586% | 1,706 |
| Remaining individualsnot grpmax-eligible | 0.016% | 6,251 |
| Admixed American | 0.0117% | 8,576 |
| South Asian | 0.00329% | 30,358 |
| European (non-Finnish) | 0.00119% | 84,287 |
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.Asp671=
- Coding
- c.2013C>T
- MANE Select
- NM_001365068
- dbSNP
- rs113540918
- Type
- single nucleotide variant
- Location
- chr9:116863610 (GRCh38)
- Gene constraint
- LOEUF 0.473 · pLI 0.99 · ClinGen HI 1/3 (gnomAD)
- Structure
- AlphaFold pLDDT 64.93 · 3 PDB
- Residue 671
- a disulfide bond; the egf-like 2 domain
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-asp671 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown