Is DMD p.Pro3409= (c.10227C>T) pathogenic?

DMD p.Pro3409= (c.10227C>T) is classified Likely benign in DMD (ClinVar, Single submitter, 1 submitter; last evaluated 2023-03-19). Very rare (popmax 0.00296%, eas); Associated with Duchenne muscular dystrophy.

What condition is associated with DMD p.Pro3409= (c.10227C>T)?

DMD p.Pro3409= (c.10227C>T) is associated with Duchenne muscular dystrophy (ClinVar).

How common is DMD p.Pro3409= (c.10227C>T) in the general population?

DMD p.Pro3409= (c.10227C>T) is very rare (popmax 0.00296%, eas) (gnomAD).

How is Duchenne muscular dystrophy inherited?

Typically X-linked recessive (Orphanet). A genetic counselor can assess individual risk for a family.

DMD p.Pro3409=

c.10227C>T · rs1256875628 · VCV1539874

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00296%, eas)

Conditions

Duchenne muscular dystrophy

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.033	moderately benign-leaning
Splicing
SpliceAI	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP 1.1	GERP -0.97, phastCons 1
Overall
CADD	4.102	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00296% East Asian · 1/33,763 alleles

Filtering AF 3.7e-05% ClinGen BA1/BS1 input FAF95, joint · FAF99 1.4e-05%

Overall 0.000249% 3/1,206,616 alleles · very rare exomes 3/1,093,461 · genomes 0/113,155 · joint denominator

Ancestry group	Frequency	1 in
East Asiangrpmax	0.00296%	33,763
European (non-Finnish)	0.000224%	446,088

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: DMD
Protein: p.Pro3409=
Coding: c.10227C>T
MANE Select: NM_004006
dbSNP: rs1256875628
Type: single nucleotide variant
Location: chrX:31177967 (GRCh38)

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

Disease context

Duchenne muscular dystrophy — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Duchenne muscular dystrophy (Orphanet):

Inheritance: X-linked recessive
Onset: Childhood
Prevalence: 1-9 / 100 000 (Worldwide)

Similar variants

DMD p.Pro3409fs Pathogenic ★★ same residue
DMD p.Pro3409Ala Uncertain significance ★ same residue
DMD p.Pro3409Ser Uncertain significance ⚠ same residue
DMD c.10086+1G>A Pathogenic ★★ same condition
DMD c.10086+1G>T Pathogenic ★★ same condition
DMD c.10086+2T>C Pathogenic ★★ same condition
DMD c.10087-2A>G Pathogenic/Likely pathogenic ★★ same condition
DMD c.10223+1G>A 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/dmd-p-pro3409 (accessed [today's date]).

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