Is MEN1 p.Pro546= (c.1638G>A) pathogenic?

MEN1 p.Pro546= (c.1638G>A) is classified Benign/Likely benign in MEN1 (ClinVar, Multiple submitters, 12 submitters; last evaluated 2026-06-01). Rare (popmax 0.185%, amr); Associated with hereditary neoplastic syndrome.

What condition is associated with MEN1 p.Pro546= (c.1638G>A)?

MEN1 p.Pro546= (c.1638G>A) is associated with hereditary neoplastic syndrome, multiple endocrine neoplasia type 1 (ClinVar).

How common is MEN1 p.Pro546= (c.1638G>A) in the general population?

MEN1 p.Pro546= (c.1638G>A) is rare (popmax 0.185%, amr) (gnomAD).

MEN1 p.Pro546=

c.1638G>A · rs368783097 · VCV215541

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 12 submitters

gnomAD v4.1

Rare

rare (popmax 0.185%, amr)

Conditions

hereditary neoplastic syndrome

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 -16	GERP -2.6
Overall
CADD	0.244	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.185% Admixed American · 111/60,026 alleles

Filtering AF 0.157% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.147%

Overall 0.00787% 127/1,614,044 alleles · rare

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.185%	541
East Asian	0.0134%	7,479
Remaining individualsnot grpmax-eligible	0.0112%	8,929
South Asian	0.0011%	91,086
European (non-Finnish)	0.000169%	590,002

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: MEN1
Protein: p.Pro546=
Coding: c.1638G>A
MANE Select: NM_001370259
dbSNP: rs368783097
Type: single nucleotide variant
Location: chr11:64804529 (GRCh38)
Gene constraint: LOEUF 0.206 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 85.13 · 69 PDB
Residue 546: the 'disordered' region

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

Disease context

hereditary neoplastic syndrome — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: multiple endocrine neoplasia type 1

Similar variants

MEN1 p.Pro546Gln Uncertain significance ★★ same residue
MEN1 p.Pro546Ser Uncertain significance ★★ same residue
MEN1 p.Pro546Leu Conflicting classifications of pathogenicity ★ same residue
MEN1 p.Pro546dup Conflicting classifications of pathogenicity ★ same residue
MEN1 c.1049+1G>A Pathogenic ★★ same condition
MEN1 c.1049+1G>C Pathogenic ★★ same condition
MEN1 c.1049+2T>C Pathogenic/Likely pathogenic ★★ same condition
MEN1 c.1350+1G>A Pathogenic ★★ 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/men1-p-pro546 (accessed [today's date]).

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