Is MEN1 p.Arg516= (c.1548G>A) pathogenic?

MEN1 p.Arg516= (c.1548G>A) is classified Likely benign in MEN1 (ClinVar, Single submitter, 1 submitter; last evaluated 2020-02-19). Absent from gnomAD v4.1.

How common is MEN1 p.Arg516= (c.1548G>A) in the general population?

MEN1 p.Arg516= (c.1548G>A) is absent from gnomAD v4.1 (gnomAD).

MEN1 p.Arg516=

c.1548G>A · rs1297016658 · VCV917713

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,608,198)

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 -0.08	GERP -3, phastCons 0.66
Overall
CADD	2.217	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

No allele count reported in gnomAD v4.1 (AN 1,608,198). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: MEN1
Protein: p.Arg516=
Coding: c.1548G>A
MANE Select: NM_001370259
dbSNP: rs1297016658
Type: single nucleotide variant
Location: chr11:64804619 (GRCh38)
Gene constraint: LOEUF 0.206 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 85.13 · 69 PDB
Residue 516: the 'disordered' region

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

Similar variants

MEN1 p.Arg516Gln Uncertain significance ★★ same residue
MEN1 p.Arg516Trp Uncertain significance ★★ ⚠ same residue
MEN1 p.Arg516Gly Conflicting classifications of pathogenicity ★ ⚠ same residue
MEN1 p.Arg516Pro Uncertain significance ★ same residue
MEN1 p.Arg516fs Pathogenic ★★ 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

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-arg516 (accessed [today's date]).

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