AMER1 p.Asp473=
c.1419C>T · VCV4727336
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.000248%)
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 | GERP -1.7, phastCons 1 |
| Overall | ||
| CADD | 4.723 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000248%
Overall
0.000248%
3/1,209,846 alleles · very rare
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
- AMER1
- Protein
- p.Asp473=
- Coding
- c.1419C>T
- MANE Select
- NM_152424
- Type
- single nucleotide variant
- Location
- chrX:64191868 (GRCh38)
- Structure
- AlphaFold pLDDT 48.88 · 3 PDB
- Residue 473
- the 'disordered' region
Similar variants
- AMER1 p.Arg353Ter Pathogenic ★★ same type
- AMER1 p.Arg358Ter Pathogenic ★★ same type
- AMER1 p.Arg497Ter Pathogenic/Likely pathogenic ★★ same type
- AMER1 p.Gln189Ter Pathogenic ★★ same type
- AMER1 p.Gln335Ter Pathogenic ★★ same type
- AMER1 p.Glu191Ter Pathogenic/Likely pathogenic ★★ same type
- AMER1 p.Ala202Gly Uncertain significance ★★ ⚠ same type
- AMER1 p.Ala229Pro 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/amer1-p-asp473 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown