Is DNM1 p.Val47= (c.141G>T) pathogenic?

DNM1 p.Val47= (c.141G>T) is classified Likely benign in DNM1 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-07-23). Very rare (popmax 0.00194%, amr); Associated with developmental and epileptic encephalopathy, 31A.

What condition is associated with DNM1 p.Val47= (c.141G>T)?

DNM1 p.Val47= (c.141G>T) is associated with developmental and epileptic encephalopathy, 31A (ClinVar).

How common is DNM1 p.Val47= (c.141G>T) in the general population?

DNM1 p.Val47= (c.141G>T) is very rare (popmax 0.00194%, amr) (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.Val47=

c.141G>T · rs1269297218 · VCV1674345

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00194%, amr)

Conditions

developmental and epileptic encephalopathy, 31A

⚠ Built without this gene's context — gene constraint and dosage, protein structure, pathways, panels and related-variant links were not looked up for this page. why

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP 7.8	GERP 2.2, phastCons 1
Overall
CADD	13.69	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00194% Admixed American · 1/51,418 alleles

Filtering AF 8.1e-05% ClinGen BA1/BS1 input FAF95, joint · FAF99 5.5e-05%

Overall 0.000389% 6/1,542,448 alleles · very rare exomes 3/1,390,470 · genomes 3/151,978 · joint denominator

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.00194%	51,418
African / African-American	0.00142%	70,176
European (non-Finnish)	0.000348%	287,498

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: DNM1
Protein: p.Val47=
Coding: c.141G>T
MANE Select: NM_004408
dbSNP: rs1269297218
Type: single nucleotide variant
Location: chr9:128203611 (GRCh38)

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)

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-val47 (accessed [today's date]).

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