AMER1 p.Arg21=
c.63T>G · rs750665616 · VCV1627925
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0415%, eas)
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 1.5 | GERP -3.3, phastCons 1 |
| Overall | ||
| CADD | 2.987 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0415%
East Asian · 14/33,718 alleles
Filtering AF
0.0251%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0201%
Overall
0.00132%
16/1,209,450 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0415% | 2,408 |
| Remaining individualsnot grpmax-eligible | 0.0042% | 23,795 |
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.Arg21=
- Coding
- c.63T>G
- MANE Select
- NM_152424
- dbSNP
- rs750665616
- Type
- single nucleotide variant
- Location
- chrX:64193224 (GRCh38)
- Structure
- AlphaFold pLDDT 48.88 · 3 PDB
- Residue 21
- the 'disordered' region
Similar variants
- AMER1 p.Arg21Cys Uncertain significance ★ ⚠ same residue
- AMER1 p.Arg21His Benign ★ ⚠ same residue
- 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
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-arg21 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown