ATRN p.Val460=
c.1380C>A · rs145699248 · VCV2190932
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0893%, afr)
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 1.1 | GERP 0.074, phastCons 1 |
| Overall | ||
| CADD | 7.944 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0893%
African / African-American · 67/75,012 alleles
Filtering AF
0.0721%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0659%
Overall
0.00458%
74/1,614,068 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0893% | 1,120 |
| Admixed American | 0.00666% | 15,004 |
| Remaining individualsnot grpmax-eligible | 0.0048% | 20,837 |
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
- ATRN
- Protein
- p.Val460=
- Coding
- c.1380C>A
- MANE Select
- NM_139321
- dbSNP
- rs145699248
- Type
- single nucleotide variant
- Location
- chr20:3560838 (GRCh38)
- Gene constraint
- LOEUF 0.395 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 79.27
Similar variants
- ATRN p.Ala438Gly Uncertain significance ★★ ⚠ same type
- ATRN p.Ala87Val Uncertain significance ★★ ⚠ same type
- ATRN p.Arg1417Gln Uncertain significance ★★ ⚠ same type
- ATRN p.Arg173His Uncertain significance ★★ ⚠ same type
- ATRN p.Asn1035Ser Uncertain significance ★★ ⚠ same type
- ATRN p.Asn213Ser Uncertain significance ★★ ⚠ same type
- ATRN p.Asn300Thr Uncertain significance ★★ ⚠ same type
- ATRN p.Asp508Asn 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/atrn-p-val460 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown