Is AMH p.Thr105Pro (c.313A>C) pathogenic?

AMH p.Thr105Pro (c.313A>C) is classified Likely benign in AMH (ClinVar, Single submitter, 1 submitter; last evaluated 2024-12-07). AlphaMissense: likely benign (0.0435); Absent from gnomAD v4.1; Associated with Inborn genetic diseases.

What condition is associated with AMH p.Thr105Pro (c.313A>C)?

AMH p.Thr105Pro (c.313A>C) is associated with Inborn genetic diseases (ClinVar).

How common is AMH p.Thr105Pro (c.313A>C) in the general population?

AMH p.Thr105Pro (c.313A>C) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about AMH p.Thr105Pro (c.313A>C)?

AlphaMissense predicts likely benign (score 0.0435) — an in-silico prediction, not a clinical call.

AMH p.Thr105Pro

c.313A>C · VCV3535621

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0435 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.0435	likely benign
REVEL	0.119	moderately benign-leaning
SaProt	LLR -7.86	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -3.5	GERP -1.6
Regional constraint	o/e 1.27	unconstrained · MANE · 2,621 bp · p 9.3e-15 · regional, not allelic
Overall
CADD	0.09	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

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: AMH
Protein: p.Thr105Pro
Coding: c.313A>C
MANE Select: NM_000479
Type: single nucleotide variant
Location: chr19:2249645 (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 105: 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

AMH p.Thr105= Likely benign ★ same residue
AMH p.Arg219His Uncertain significance ★★ ⚠ same condition
AMH p.Asp192Gly Uncertain significance ★★ ⚠ same condition
AMH p.Glu256Gln Uncertain significance ★★ ⚠ same condition
AMH p.Pro168Thr Uncertain significance ★★ ⚠ same condition
AMH p.Pro46His Uncertain significance ★★ ⚠ same condition
AMH p.Thr268Ala Uncertain significance ★★ ⚠ same condition
AMH p.Ala162Val 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-thr105pro (accessed [today's date]).

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