AMER1 p.Ser47=
c.141C>T · rs187016794 · VCV2179251
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00881%, sas)
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 -0.088 | GERP -3.4, phastCons 0.017 |
| Overall | ||
| CADD | 2.102 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00881%
South Asian · 5/56,777 alleles
Filtering AF
0.0034%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00217%
Overall
0.0014%
17/1,210,292 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.00881% | 11,355 |
| African / African-American | 0.00873% | 11,459 |
| Admixed American | 0.00437% | 22,895 |
| European (non-Finnish) | 0.000558% | 179,069 |
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.Ser47=
- Coding
- c.141C>T
- MANE Select
- NM_152424
- dbSNP
- rs187016794
- Type
- single nucleotide variant
- Location
- chrX:64193146 (GRCh38)
- Structure
- AlphaFold pLDDT 48.88 · 3 PDB
- Residue 47
- 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-ser47 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown