AMH p.Ala463=
c.1389G>C · VCV3672729
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.358%, 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 -2 | GERP -2 |
| Overall | ||
| CADD | 8.531 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.358%
East Asian · 159/44,382 alleles
Filtering AF
0.313%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.295%
Overall
0.0104%
167/1,605,868 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.358% | 279 |
| Remaining individualsnot grpmax-eligible | 0.00804% | 12,432 |
| Admixed American | 0.00167% | 59,710 |
| Finnishnot grpmax-eligible | 0.00163% | 61,176 |
| South Asian | 0.0011% | 90,604 |
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
- AMH
- Protein
- p.Ala463=
- Coding
- c.1389G>C
- MANE Select
- NM_000479
- Type
- single nucleotide variant
- Location
- chr19:2251663 (GRCh38)
- Gene constraint
- LOEUF 1.954 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 69.40 · 3 PDB
- Residue 463
- a disulfide bond; a β-strand
Similar variants
- AMH p.Ala463Val Uncertain significance ★ ⚠ same residue
- AMH p.Arg40Ter Pathogenic/Likely pathogenic ★★ same type
- AMH p.Gln217Ter Pathogenic/Likely pathogenic ★★ same type
- AMH p.Glu389Ter Pathogenic/Likely pathogenic ★★ same type
- AMH p.Gly101Arg Likely pathogenic ★★ same type
- AMH p.Pro151Ser Pathogenic ★★ ⚠ same type
- AMH p.Trp371Ter Pathogenic ★★ same type
- AMH p.Tyr167Cys 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/amh-p-ala463 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown