Is DNM2 p.Asp720= (c.2160C>T) pathogenic?

DNM2 p.Asp720= (c.2160C>T) is classified Benign/Likely benign in DNM2 (ClinVar, Multiple submitters, 11 submitters; last evaluated 2026-02-01). Low-frequency (popmax 1.65%, eas); Associated with Inborn genetic diseases.

What condition is associated with DNM2 p.Asp720= (c.2160C>T)?

DNM2 p.Asp720= (c.2160C>T) is associated with Inborn genetic diseases, autosomal dominant centronuclear myopathy, Charcot-Marie-Tooth disease dominant intermediate B (ClinVar).

How common is DNM2 p.Asp720= (c.2160C>T) in the general population?

DNM2 p.Asp720= (c.2160C>T) is low-frequency (popmax 1.65%, eas) (gnomAD).

DNM2 p.Asp720=

c.2160C>T · rs117598326 · VCV238207

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 11 submitters

gnomAD v4.1

Rare

low-frequency (popmax 1.65%, eas)

Conditions

Inborn genetic diseases

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 -8.7	GERP -3.7
Overall
CADD	7.864	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 1.65% East Asian · 741/44,868 alleles

Filtering AF 1.55% ClinGen BA1/BS1 input FAF95, joint · FAF99 1.51%

Overall 0.15% 2,413/1,613,804 alleles · low-frequency exomes 2,253/1,461,482 · genomes 160/152,322 · joint denominator

Ancestry group	Frequency	1 in
East Asiangrpmax	1.65%	61
Remaining individualsnot grpmax-eligible	0.221%	453
South Asian	0.148%	675
European (non-Finnish)	0.117%	856
African / African-American	0.016%	6,254
Finnishnot grpmax-eligible	0.00941%	10,625
Admixed American	0.005%	20,005

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: DNM2
Protein: p.Asp720=
Coding: c.2160C>T
MANE Select: NM_001005361
dbSNP: rs117598326
Type: single nucleotide variant
Location: chr19:10829137 (GRCh38)
Gene constraint: LOEUF 0.239 · pLI 1.00 · ClinGen HI 0/3 (gnomAD)
Structure: AlphaFold pLDDT 78.38 · 1 PDB
Residue 720: the ged domain

Full DNM2 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: autosomal dominant centronuclear myopathy Charcot-Marie-Tooth disease dominant intermediate B fetal akinesia-cerebral and retinal hemorrhage syndrome

Similar variants

DNM2 p.Asp720Asn Uncertain significance ★ ⚠ same residue
DNM2 p.Asp720fs Uncertain significance ★ same residue
DNM2 p.Ala618Thr Pathogenic ★★★ same condition
DNM2 p.Arg369Gln Pathogenic ★★★ ⚠ same condition
DNM2 p.Arg369Trp Pathogenic ★★★ same condition
DNM2 p.Arg465Trp Pathogenic ★★★ same condition
DNM2 p.Arg522Cys Likely pathogenic ★★★ same condition
DNM2 p.Arg522His 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/dnm2-p-asp720 (accessed [today's date]).

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