Is EMD p.Tyr155= (c.465C>T) pathogenic?

EMD p.Tyr155= (c.465C>T) is classified Benign/Likely benign in EMD (ClinVar, Multiple submitters, 15 submitters; last evaluated 2026-02-03). Low-frequency (popmax 1.19%, afr); Associated with Emery-Dreifuss muscular dystrophy 1, X-linked.

What condition is associated with EMD p.Tyr155= (c.465C>T)?

EMD p.Tyr155= (c.465C>T) is associated with Emery-Dreifuss muscular dystrophy 1, X-linked, cardiomyopathy, X-linked Emery-Dreifuss muscular dystrophy (ClinVar).

How common is EMD p.Tyr155= (c.465C>T) in the general population?

EMD p.Tyr155= (c.465C>T) is low-frequency (popmax 1.19%, afr) (gnomAD).

EMD p.Tyr155=

c.465C>T · rs143447675 · VCV42274

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 15 submitters

gnomAD v4.1

Rare

low-frequency (popmax 1.19%, afr)

Conditions

Emery-Dreifuss muscular dystrophy 1, X-linked

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 · C>G here scores Δ0.21 · evaluated, not missing
Constraint at this position
Conservation	phyloP -2.1	GERP -3
Overall
CADD	0.252	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 1.19% African / African-American · 686/57,429 alleles

Filtering AF 1.12% ClinGen BA1/BS1 input FAF95, joint · FAF99 1.09%

Overall 0.0721% 873/1,210,507 alleles · low-frequency

Ancestry group	Frequency	1 in
African / African-Americangrpmax	1.19%	84
Admixed American	0.15%	666
Remaining individualsnot grpmax-eligible	0.115%	866
Middle Eastern	0.023%	4,355
European (non-Finnish)	0.00693%	14,439

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.Tyr155=
Coding: c.465C>T
MANE Select: NM_000117
dbSNP: rs143447675
Type: single nucleotide variant
Location: chrX:154380897 (GRCh38)
Structure: AlphaFold pLDDT 61.26 · 6 PDB
Residue 155: the 'interaction with f-actin' region

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

Disease context

Emery-Dreifuss muscular dystrophy 1, X-linked — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: cardiomyopathy X-linked Emery-Dreifuss muscular dystrophy

Similar variants

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
EMD c.399+1G>T Pathogenic ★★ same condition
EMD c.399+2T>C Pathogenic ★★ same condition
EMD c.450-2A>G Pathogenic/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/emd-p-tyr155 (accessed [today's date]).

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