Is DTNA p.Arg63= (c.187C>A) pathogenic?

DTNA p.Arg63= (c.187C>A) is classified Likely benign in DTNA (ClinVar, Single submitter, 1 submitter; last evaluated 2025-02-06). Very rare (popmax 0.00223%, eas); Associated with left ventricular noncompaction 1.

What condition is associated with DTNA p.Arg63= (c.187C>A)?

DTNA p.Arg63= (c.187C>A) is associated with left ventricular noncompaction 1 (ClinVar).

How common is DTNA p.Arg63= (c.187C>A) in the general population?

DTNA p.Arg63= (c.187C>A) is very rare (popmax 0.00223%, eas) (gnomAD).

How is Left ventricular noncompaction inherited?

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

DTNA p.Arg63=

c.187C>A · rs773407468 · VCV1592120

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00223%, eas)

Conditions

left ventricular noncompaction 1

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 0.082	GERP 1.9, phastCons 0.81
Overall
CADD	8.207	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00223% East Asian · 1/44,866 alleles

Filtering AF 6.8e-05% ClinGen BA1/BS1 input FAF95, joint · FAF99 1.9e-05%

Overall 0.000372% 6/1,613,902 alleles · very rare

Ancestry group	Frequency	1 in
East Asiangrpmax	0.00223%	44,866
African / African-American	0.00134%	74,902
South Asian	0.0011%	91,072
European (non-Finnish)	0.000254%	393,335

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: DTNA
Protein: p.Arg63=
Coding: c.187C>A
MANE Select: NM_001386795
dbSNP: rs773407468
Type: single nucleotide variant
Location: chr18:34794075 (GRCh38)
Gene constraint: LOEUF 0.523 · pLI 0.40 (gnomAD)
Structure: AlphaFold pLDDT 69.98 · 1 PDB
Residue 63: the 'interaction with magee1' region

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

Disease context

left ventricular noncompaction 1 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Left ventricular noncompaction (Orphanet):

Inheritance: Autosomal dominant, Autosomal recessive, Mitochondrial inheritance
Onset: All ages

Similar variants

DTNA p.Arg63Gln Uncertain significance ★★ ⚠ same residue
DTNA p.Arg63Gly Uncertain significance ★ ⚠ same residue
DTNA c.1346+5G>C Uncertain significance ★★ same condition
DTNA c.362+1G>A Uncertain significance ★★ same condition
DTNA c.604-13T>G Uncertain significance ★★ same condition
DTNA p.Ala118Thr Uncertain significance ★★ ⚠ same condition
DTNA p.Ala232Val Uncertain significance ★★ ⚠ same condition
DTNA p.Ala302Thr 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/dtna-p-arg63 (accessed [today's date]).

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