ATRN p.Val1406=
c.4218G>A · rs373572320 · VCV2186804
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0138%, nfe)
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 0.12 | GERP -4.1, phastCons 0.72 |
| Overall | ||
| CADD | 2.974 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0138%
European (non-Finnish) · 162/1,177,796 alleles
Filtering AF
0.012%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0114%
Overall
0.0102%
164/1,609,086 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.0138% | 7,270 |
| Remaining individualsnot grpmax-eligible | 0.00161% | 62,290 |
| African / African-American | 0.00134% | 74,860 |
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.Val1406=
- Coding
- c.4218G>A
- MANE Select
- NM_139321
- dbSNP
- rs373572320
- Type
- single nucleotide variant
- Location
- chr20:3646775 (GRCh38)
- Gene constraint
- LOEUF 0.395 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 79.27
Similar variants
- ATRN p.Val1406Ala Uncertain significance ★★ ⚠ same residue
- 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
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-val1406 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown