Is MEN1 p.Ala307Pro (c.919G>C) pathogenic?

MEN1 p.Ala307Pro (c.919G>C) is classified Uncertain significance in MEN1 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-12-21). AlphaMissense: likely pathogenic (0.9605); Absent from gnomAD v4.1.

How common is MEN1 p.Ala307Pro (c.919G>C) in the general population?

MEN1 p.Ala307Pro (c.919G>C) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about MEN1 p.Ala307Pro (c.919G>C)?

AlphaMissense predicts likely pathogenic (score 0.9605) — an in-silico prediction, not a clinical call.

MEN1 p.Ala307Pro

c.919G>C · VCV4912208

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.9605 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Computational evidence

Protein change
AlphaMissense	0.9605	likely pathogenic
REVEL	0.528	indeterminate
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 3.2	GERP -0.03, phastCons 1
Regional constraint	o/e 0.61	unconstrained · MANE · 4,962 bp · p 4.4e-20 · regional, not allelic
Overall
CADD	22.7	PHRED · no single calibrated threshold — expert panels disagree

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

⚠ Isoform check: AlphaMissense numbered on a different transcript (AM A312P vs ClinVar A307P) — verify the residue.

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: MEN1
Protein: p.Ala307Pro
Coding: c.919G>C
MANE Select: NM_001370259
Type: single nucleotide variant
Location: chr11:64806362 (GRCh38)
Gene constraint: LOEUF 0.206 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 85.13 · 69 PDB
Residue 307: the 'interaction with fancd2' region; an α-helix

Full MEN1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

MEN1 p.Ala307= Likely benign ★★ same residue
MEN1 p.Ala307Asp Conflicting classifications of pathogenicity ★ same residue
MEN1 p.Ala307Val Uncertain significance ★ same residue
MEN1 c.1049+1G>A Pathogenic ★★ same type
MEN1 c.1049+1G>C Pathogenic ★★ same type
MEN1 c.1049+2T>C Pathogenic/Likely pathogenic ★★ same type
MEN1 c.1350+1G>A Pathogenic ★★ same type
MEN1 c.1351-2A>C Pathogenic/Likely 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/men1-p-ala307pro (accessed [today's date]).

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