Is MEN1 p.462AEA[3] (c.1383GGCCGAGGC[3]) pathogenic?

MEN1 p.462AEA[3] (c.1383GGCCGAGGC[3]) is classified Uncertain significance in MEN1 (ClinVar, Multiple submitters, 3 submitters; last evaluated 2024-04-25). Ultra-rare (gnomAD MAF 6.705e-06); Associated with multiple endocrine neoplasia type 1.

What condition is associated with MEN1 p.462AEA[3] (c.1383GGCCGAGGC[3])?

MEN1 p.462AEA[3] (c.1383GGCCGAGGC[3]) is associated with multiple endocrine neoplasia type 1, hereditary neoplastic syndrome (ClinVar).

How common is MEN1 p.462AEA[3] (c.1383GGCCGAGGC[3]) in the general population?

MEN1 p.462AEA[3] (c.1383GGCCGAGGC[3]) is ultra-rare (gnomAD MAF 6.705e-06) (gnomAD).

How is Multiple endocrine neoplasia type 1 inherited?

Typically Autosomal dominant, Not applicable (Orphanet). A genetic counselor can assess individual risk for a family.

MEN1 p.462AEA[3]

c.1383GGCCGAGGC[3] · rs772978541 · VCV1372356

Uncertain significance Multiple submitters

Classification

Uncertain significance

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

gnomAD v4.1

Rare

ultra-rare (gnomAD MAF 6.705e-06)

Conditions

multiple endocrine neoplasia type 1

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP -16	GERP -3

Population frequency

dbSNP / gnomAD

Global frequency 0.00067% via dbSNP · ultra-rare

No ancestry breakdown or filtering allele frequency is available for this variant, so BA1/BS1 cannot be assessed from this figure alone.

Variant & gene context

Gene: MEN1
Protein: p.462AEA[3]
Coding: c.1383GGCCGAGGC[3]
MANE Select: NM_001370259
dbSNP: rs772978541
Type: Microsatellite
Location: chr11:64804766 (GRCh38)
Gene constraint: LOEUF 0.206 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 85.13 · 69 PDB

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

Disease context

multiple endocrine neoplasia type 1 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: hereditary neoplastic syndrome

For Multiple endocrine neoplasia type 1 (Orphanet):

Inheritance: Autosomal dominant, Not applicable
Onset: All ages
Prevalence: 1-9 / 100 000 (Europe)

Similar variants

MEN1 p.Ala242fs Pathogenic ★★ same condition
MEN1 p.Asp70fs Pathogenic ★★ same condition
MEN1 p.Glu425del Pathogenic/Likely pathogenic ★★ same condition
MEN1 p.Lys120del Pathogenic ★★ same condition
MEN1 p.Ser512fs Pathogenic ★★ same condition
MEN1 p.Leu600fs Uncertain significance ★★ same condition
MEN1 p.Lys589del Uncertain significance ★★ same condition
MEN1 c.1351-24_1351-14del Benign/Likely benign ★★ 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-462aea-3 (accessed [today's date]).

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