Is DNM1 p.Asp28= (c.84C>T) pathogenic?

DNM1 p.Asp28= (c.84C>T) is classified Benign in DNM1 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2023-03-26). Ultra-rare (popmax 0.0826%, sas); Associated with Inborn genetic diseases.

What condition is associated with DNM1 p.Asp28= (c.84C>T)?

DNM1 p.Asp28= (c.84C>T) is associated with Inborn genetic diseases, developmental and epileptic encephalopathy, 31A (ClinVar).

How common is DNM1 p.Asp28= (c.84C>T) in the general population?

DNM1 p.Asp28= (c.84C>T) is ultra-rare (popmax 0.0826%, sas) (gnomAD).

DNM1 p.Asp28=

c.84C>T · rs577437504 · VCV1763636

Benign Multiple submitters

Classification

Benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

ultra-rare (popmax 0.0826%, sas)

Conditions

Inborn genetic diseases

⚠ 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 4.5	GERP 1.2, phastCons 1
Overall
CADD	14.62	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0826% South Asian · 70/84,796 alleles

Filtering AF 0.0669% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0613%

Overall 0.00491% 76/1,549,390 alleles · ultra-rare exomes 69/1,397,356 · genomes 7/152,034 · joint denominator

Ancestry group	Frequency	1 in
South Asiangrpmax	0.0826%	1,211
Remaining individualsnot grpmax-eligible	0.00673%	14,853
East Asian	0.00269%	37,214
European (non-Finnish)	8.69e-05%	1,151,349

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.Asp28=
Coding: c.84C>T
MANE Select: NM_004408
dbSNP: rs577437504
Type: single nucleotide variant
Location: chr9:128203554 (GRCh38)

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

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: developmental and epileptic encephalopathy, 31A

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-asp28 (accessed [today's date]).

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