ASTN1 p.Glu962Val
c.2885A>T · rs543065232 · VCV2339931
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0917%, amr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.104 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 7.8 | GERP 2.5, phastCons 1 |
| Regional constraint | o/e 0.93 | unconstrained · MANE · 85 kb · p 0.052 · regional, not allelic |
| Overall | ||
| CADD | 26.5 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0917%
Admixed American · 55/60,004 alleles
Filtering AF
0.0722%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0653%
Overall
0.00446%
72/1,613,946 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0917% | 1,091 |
| European (non-Finnish) | 0.00144% | 69,413 |
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
- ASTN1
- Protein
- p.Glu962Val
- Coding
- c.2885A>T
- MANE Select
- NM_004319
- dbSNP
- rs543065232
- Type
- single nucleotide variant
- Location
- chr1:176894617 (GRCh38)
- Gene constraint
- LOEUF 0.392 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 64.88
Similar variants
- ASTN1 p.Asp1150Tyr Uncertain significance ★★ same type
- ASTN1 p.His419Asn Uncertain significance ★★ same type
- ASTN1 p.Ser290Gly Uncertain significance ★★ same type
- ASTN1 p.Val1025Leu Uncertain significance ★★ same type
- ASTN1 p.Arg1112Ter Likely pathogenic ★ same type
- ASTN1 p.Gly742Arg Likely pathogenic ★ same type
- ASTN1 c.1523+1G>T Uncertain significance ★ same type
- ASTN1 p.Ala2Thr Uncertain significance ★ 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/astn1-p-glu962val (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown