Is MEN1 p.Gln536= (c.1608G>A) pathogenic?

MEN1 p.Gln536= (c.1608G>A) is classified Benign/Likely benign in MEN1 (ClinVar, Multiple submitters, 6 submitters; last evaluated 2026-01-11). Very rare (popmax 0.005%, amr); Associated with hereditary neoplastic syndrome.

What condition is associated with MEN1 p.Gln536= (c.1608G>A)?

MEN1 p.Gln536= (c.1608G>A) is associated with hereditary neoplastic syndrome, multiple endocrine neoplasia type 1 (ClinVar).

How common is MEN1 p.Gln536= (c.1608G>A) in the general population?

MEN1 p.Gln536= (c.1608G>A) is very rare (popmax 0.005%, amr) (gnomAD).

MEN1 p.Gln536=

c.1608G>A · rs1055457298 · VCV457308

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 6 submitters

gnomAD v4.1

Rare

very rare (popmax 0.005%, 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 -4.1	GERP -2.6
Overall
CADD	0.112	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.005% Admixed American · 3/60,004 alleles

Filtering AF 0.00133% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000668%

Overall 0.000806% 13/1,613,280 alleles · very rare

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.005%	20,001
European (non-Finnish)	0.000847%	117,997

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.Gln536=
Coding: c.1608G>A
MANE Select: NM_001370259
dbSNP: rs1055457298
Type: single nucleotide variant
Location: chr11:64804559 (GRCh38)
Gene constraint: LOEUF 0.206 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 85.13 · 69 PDB
Residue 536: 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.Gln536Arg Uncertain significance ★★ same residue
MEN1 p.Gln536Glu Uncertain significance ★★ same residue
MEN1 p.Gln536Leu Uncertain significance ★★ same residue
MEN1 p.Gln536Ter Pathogenic ★ 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-gln536 (accessed [today's date]).

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