Is EMD p.Asp136= (c.408T>C) pathogenic?

EMD p.Asp136= (c.408T>C) is classified Conflicting classifications of pathogenicity in EMD (ClinVar, Conflicting submitters, 2 submitters; last evaluated 2023-12-12). Very rare (popmax 9.11e-05%); Associated with X-linked Emery-Dreifuss muscular dystrophy.

What condition is associated with EMD p.Asp136= (c.408T>C)?

EMD p.Asp136= (c.408T>C) is associated with X-linked Emery-Dreifuss muscular dystrophy (ClinVar).

How common is EMD p.Asp136= (c.408T>C) in the general population?

EMD p.Asp136= (c.408T>C) is very rare (popmax 9.11e-05%) (gnomAD).

How is Emery-Dreifuss muscular dystrophy inherited?

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

EMD p.Asp136=

c.408T>C · rs1569552096 · VCV594142

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

very rare (popmax 9.11e-05%)

Conditions

X-linked Emery-Dreifuss muscular dystrophy

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 -0.79	GERP -2.8, phastCons 0.02
Overall
CADD	3.093	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 9.11e-05%

Overall 9.11e-05% 1/1,097,996 alleles · very 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.Asp136=
Coding: c.408T>C
MANE Select: NM_000117
dbSNP: rs1569552096
Type: single nucleotide variant
Location: chrX:154380761 (GRCh38)
Structure: AlphaFold pLDDT 61.26 · 6 PDB
Residue 136: the 'interaction with f-actin' region

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

Disease context

X-linked Emery-Dreifuss muscular dystrophy — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Emery-Dreifuss muscular dystrophy (Orphanet):

Inheritance: Autosomal dominant, Autosomal recessive, X-linked recessive
Onset: Childhood
Prevalence: 1-9 / 1 000 000 (Europe)

Similar variants

EMD p.Asp136His Uncertain significance ★★ ⚠ same residue
EMD p.Asp136Asn Uncertain significance ★ ⚠ same residue
EMD p.Asp136fs Likely pathogenic ★ 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
EMD c.266-3A>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-asp136 (accessed [today's date]).

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