Is EMD p.Asp137= (c.411C>T) pathogenic?

EMD p.Asp137= (c.411C>T) is classified Likely benign in EMD (ClinVar, Multiple submitters, 3 submitters; last evaluated 2026-05-01). Ultra-rare (popmax 0.0232%, mid); Associated with Cardiovascular phenotype.

What condition is associated with EMD p.Asp137= (c.411C>T)?

EMD p.Asp137= (c.411C>T) is associated with Cardiovascular phenotype, X-linked Emery-Dreifuss muscular dystrophy (ClinVar).

How common is EMD p.Asp137= (c.411C>T) in the general population?

EMD p.Asp137= (c.411C>T) is ultra-rare (popmax 0.0232%, mid) (gnomAD).

EMD p.Asp137=

c.411C>T · rs2148128718 · VCV1597339

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

gnomAD v4.1

Rare

ultra-rare (popmax 0.0232%, mid)

Conditions

Cardiovascular phenotype

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 -1.2	GERP -1.9
Overall
CADD	2.616	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0232% Middle Eastern · 1/4,312 alleles

Overall 9.11e-05% 1/1,098,006 alleles · ultra-rare

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: EMD
Protein: p.Asp137=
Coding: c.411C>T
MANE Select: NM_000117
dbSNP: rs2148128718
Type: single nucleotide variant
Location: chrX:154380764 (GRCh38)
Structure: AlphaFold pLDDT 61.26 · 6 PDB
Residue 137: the 'interaction with f-actin' region

Full EMD 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: X-linked Emery-Dreifuss muscular dystrophy

Similar variants

EMD p.Asp137Asn Uncertain significance ★ ⚠ same residue
EMD p.Asp137Glu Uncertain significance ★ ⚠ same residue
EMD p.Asp137Gly Uncertain significance ★ ⚠ same residue
EMD p.Asp137_Asp138del Uncertain significance ★ same residue
EMD c.187+1G>A Pathogenic ★★ same condition
EMD c.187+1G>T Pathogenic/Likely pathogenic ★★ same condition
EMD c.265+1G>A Likely pathogenic ★★ same condition
EMD c.266-2A>G 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/emd-p-asp137 (accessed [today's date]).

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