Is AMH p.Ala162Val (c.485C>T) pathogenic?

AMH p.Ala162Val (c.485C>T) is classified Uncertain significance in AMH (ClinVar, Single submitter, 1 submitter; last evaluated 2025-08-22). AlphaMissense: likely benign (0.2671); Very rare (popmax 0.0037%, amr); Associated with Inborn genetic diseases.

What condition is associated with AMH p.Ala162Val (c.485C>T)?

AMH p.Ala162Val (c.485C>T) is associated with Inborn genetic diseases (ClinVar).

How common is AMH p.Ala162Val (c.485C>T) in the general population?

AMH p.Ala162Val (c.485C>T) is very rare (popmax 0.0037%, amr) (gnomAD).

What do computational predictors say about AMH p.Ala162Val (c.485C>T)?

AlphaMissense predicts likely benign (score 0.2671) — an in-silico prediction, not a clinical call.

AMH p.Ala162Val

c.485C>T · VCV4091688

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.2671 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.0037%, amr)

Missense predictors

1/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.2671	likely benign
REVEL	0.163	moderately benign-leaning
SaProt	LLR -10.27	damaging
⇒ SaProt calls this damaging; AlphaMissense and REVEL do not.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 2.6	GERP 0.79, phastCons 0.99
Regional constraint	o/e 1.27	unconstrained · MANE · 2,621 bp · p 9.3e-15 · regional, not allelic
Overall
CADD	22.0	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0037% Admixed American · 2/54,088 alleles

Filtering AF 0.000613% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000229%

Overall 0.000211% 3/1,420,996 alleles · very rare

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.0037%	27,044
South Asian	0.00117%	85,836

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.Ala162Val
Coding: c.485C>T
MANE Select: NM_000479
Type: single nucleotide variant
Location: chr19:2250409 (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 162: a disulfide bond

Full AMH gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

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AMH p.Ala204Val Uncertain significance ★ ⚠ same condition

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-ala162val (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown