Is DMD p.Pro1320= (c.3960A>G) pathogenic?

DMD p.Pro1320= (c.3960A>G) is classified Benign/Likely benign in DMD (ClinVar, Multiple submitters, 4 submitters; last evaluated 2026-01-20). Ultra-rare (popmax 0.046%, mid); Associated with Cardiovascular phenotype.

What condition is associated with DMD p.Pro1320= (c.3960A>G)?

DMD p.Pro1320= (c.3960A>G) is associated with Cardiovascular phenotype, cardiomyopathy, Becker muscular dystrophy (ClinVar).

How common is DMD p.Pro1320= (c.3960A>G) in the general population?

DMD p.Pro1320= (c.3960A>G) is ultra-rare (popmax 0.046%, mid) (gnomAD).

DMD p.Pro1320=

c.3960A>G · rs765256995 · VCV526136

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 4 submitters

gnomAD v4.1

Rare

ultra-rare (popmax 0.046%, mid)

Conditions

Cardiovascular phenotype

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	<0.2	all four deltas below 0.2 · T>A here scores Δ0.25 · evaluated, not missing
Constraint at this position
Conservation	phyloP -7	GERP -4.8
Overall
CADD	1.591	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.046% Middle Eastern · 2/4,352 alleles

Filtering AF 0.00813% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0034%

Overall 0.00264% 32/1,210,079 alleles · ultra-rare

Ancestry group	Frequency	1 in
Middle Easterngrpmax	0.046%	2,176
Ashkenazi Jewishnot grpmax-eligible	0.0363%	2,753
Admixed American	0.00656%	15,250
Remaining individualsnot grpmax-eligible	0.0042%	23,807
European (non-Finnish)	0.0019%	52,656

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.Pro1320=
Coding: c.3960A>G
MANE Select: NM_004006
dbSNP: rs765256995
Type: single nucleotide variant
Location: chrX:32438352 (GRCh38)

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

Disease context

Cardiovascular phenotype — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: cardiomyopathy Becker muscular dystrophy Duchenne muscular dystrophy

Similar variants

DMD p.Pro1320Arg Conflicting classifications of pathogenicity ★ ⚠ 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
DMD c.10223+1G>C Pathogenic ★★ same condition
DMD c.10224-2A>G Likely 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-pro1320 (accessed [today's date]).

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