AMH p.Val138=
c.414G>A · VCV4755171
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00341%, amr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · G>C here scores Δ0.20 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 6.3 | GERP 0.79, phastCons 1 |
| Overall | ||
| CADD | 14.15 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00341%
Admixed American · 2/58,568 alleles
Filtering AF
0.0013%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00109%
Overall
0.00169%
27/1,596,576 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.00341% | 29,284 |
| Remaining individualsnot grpmax-eligible | 0.00323% | 30,938 |
| European (non-Finnish) | 0.00196% | 51,108 |
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.Val138=
- Coding
- c.414G>A
- MANE Select
- NM_000479
- Type
- single nucleotide variant
- Location
- chr19:2250338 (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 138
- a disulfide bond
Similar variants
- 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
- AMH p.Ala78Thr 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/amh-p-val138 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown