Is MEN1 c.783+2del pathogenic?

MEN1 c.783+2del is classified Likely pathogenic in MEN1 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-05-26). Absent from gnomAD; Associated with multiple endocrine neoplasia type 1.

What condition is associated with MEN1 c.783+2del?

MEN1 c.783+2del is associated with multiple endocrine neoplasia type 1 (ClinVar).

How common is MEN1 c.783+2del in the general population?

MEN1 c.783+2del is absent from gnomAD (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 c.783+2del

rs2497202890 · VCV1999124

Likely pathogenic Single submitter

Classification

Likely pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

canonical splice-site (±1/±2)

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

multiple endocrine neoplasia type 1

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	canonical splice-site (±1/±2)	predicted loss-of-function in a haploinsufficient gene (ClinGen)
Splicing
Splice region	donor +2	canonical splice dinucleotide (donor +2) · inside the BP7-excluded zone
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP -0.38	GERP -3, phastCons 0.035
Non-coding constraint	Z 4.86	1 kb window · o/e 0.68 · regional · uncalibrated

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. 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
Coding: c.783+2del
MANE Select: NM_001370259
dbSNP: rs2497202890
Type: Deletion
Location: chr11:64807550 (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

For Multiple endocrine neoplasia type 1 (Orphanet):

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

Similar variants

MEN1 c.1350+1_1350+11del Pathogenic ★★ same condition
MEN1 c.1351-3_1359del Pathogenic/Likely pathogenic ★★ same condition
MEN1 c.1356_1367del12 Pathogenic ★★ same condition
MEN1 p.Ala176fs Pathogenic ★★ same condition
MEN1 p.Ala6fs Pathogenic ★★ same condition
MEN1 p.Arg115fs Pathogenic ★★ same condition
MEN1 p.Arg275fs Pathogenic ★★ same condition
MEN1 p.Arg479fs 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-c-783-plus-2del (accessed [today's date]).

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