Is MEN1 p.Ala5= (c.15C>T) pathogenic?

MEN1 p.Ala5= (c.15C>T) is classified Benign/Likely benign in MEN1 (ClinVar, Multiple submitters, 4 submitters; last evaluated 2025-05-25). Very rare (popmax 0.00112%, sas); Associated with hereditary neoplastic syndrome.

What condition is associated with MEN1 p.Ala5= (c.15C>T)?

MEN1 p.Ala5= (c.15C>T) is associated with hereditary neoplastic syndrome, multiple endocrine neoplasia type 1 (ClinVar).

How common is MEN1 p.Ala5= (c.15C>T) in the general population?

MEN1 p.Ala5= (c.15C>T) is very rare (popmax 0.00112%, sas) (gnomAD).

MEN1 p.Ala5=

c.15C>T · rs757821521 · VCV2904554

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 4 submitters

gnomAD v4.1

Rare

very rare (popmax 0.00112%, sas)

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 1.7	GERP 0.54, phastCons 1
Overall
CADD	14.47	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00112% South Asian · 1/89,326 alleles

Filtering AF 2.8e-05% ClinGen BA1/BS1 input FAF95, joint · FAF99 1.1e-05%

Overall 0.000188% 3/1,595,886 alleles · very rare exomes 3/1,443,814 · genomes 0/152,072 · joint denominator

Ancestry group	Frequency	1 in
South Asiangrpmax	0.00112%	89,326
European (non-Finnish)	0.00017%	587,147

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.Ala5=
Coding: c.15C>T
MANE Select: NM_001370259
dbSNP: rs757821521
Type: single nucleotide variant
Location: chr11:64810095 (GRCh38)
Gene constraint: LOEUF 0.206 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 85.13 · 69 PDB
Residue 5: an α-helix

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.Ala5Val Uncertain significance ★★ ⚠ same residue
MEN1 p.Ala5Gly Uncertain significance ★ ⚠ same residue
MEN1 p.Ala5Thr Uncertain significance ★ ⚠ 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
MEN1 c.1351-2A>C Pathogenic/Likely 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-ala5 (accessed [today's date]).

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