Is DNM1 p.Arg792fs (c.2375_2393del) pathogenic?

DNM1 p.Arg792fs (c.23752393del) is classified Uncertain significance in DNM1 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-01-05). No gnomAD frequency available for this variant; Associated with developmental and epileptic encephalopathy, 31A.

What condition is associated with DNM1 p.Arg792fs (c.2375_2393del)?

DNM1 p.Arg792fs (c.2375_2393del) is associated with developmental and epileptic encephalopathy, 31A (ClinVar).

How common is DNM1 p.Arg792fs (c.2375_2393del) in the general population?

DNM1 p.Arg792fs (c.2375_2393del) is no gnomAD frequency available for this variant (gnomAD).

How is Lennox-Gastaut syndrome inherited?

Typically Autosomal dominant, Multigenic/multifactorial (Orphanet). A genetic counselor can assess individual risk for a family.

DNM1 p.Arg792fs

c.2375_2393del · rs2539127769 · VCV2826338

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

developmental and epileptic encephalopathy, 31A

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function in a LoF-intolerant gene
NMD	predicted	premature termination codon in exon 21 of 22
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 11	GERP 1.8, phastCons 1

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: DNM1
Protein: p.Arg792fs
Coding: c.2375_2393del
MANE Select: NM_004408
dbSNP: rs2539127769
Type: Deletion
Location: chr9:128250777 (GRCh38)
Gene constraint: LOEUF 0.417 · pLI 1.00 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 78.87 · 22 PDB
Residue 792: a UniProt-annotated variant site (in dee31b); the 'disordered' region

Full DNM1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

developmental and epileptic encephalopathy, 31A — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Lennox-Gastaut syndrome (Orphanet):

Inheritance: Autosomal dominant, Multigenic/multifactorial, Not applicable
Onset: Childhood, Infancy
Prevalence: 1-9 / 1 000 000 (Europe)

Similar variants

DNM1 c.1493+14del Benign/Likely benign ★★ same condition
DNM1 p.Arg256fs Pathogenic ★ same condition
DNM1 p.Gly139_Thr141del Likely pathogenic ★ same condition
DNM1 p.Leu69fs Likely pathogenic ★ same condition
DNM1 p.Pro790fs Likely pathogenic ★ same condition
DNM1 p.Trp542fs Pathogenic ★ same condition
DNM1 c.1422+5del Uncertain significance ★ same condition
DNM1 c.993-13_993-11del Uncertain significance ★ 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/dnm1-p-arg792fs (accessed [today's date]).

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