Is EMD p.Gly216Arg (c.646G>A) pathogenic?

EMD p.Gly216Arg (c.646G>A) is classified Conflicting classifications of pathogenicity in EMD (ClinVar, Conflicting submitters, 7 submitters; last evaluated 2026-03-23). AlphaMissense: likely benign (0.1866); Rare (popmax 0.118%, afr); Associated with Cardiovascular phenotype.

What condition is associated with EMD p.Gly216Arg (c.646G>A)?

EMD p.Gly216Arg (c.646G>A) is associated with Cardiovascular phenotype, X-linked Emery-Dreifuss muscular dystrophy, Emery-Dreifuss muscular dystrophy 1, X-linked (ClinVar).

How common is EMD p.Gly216Arg (c.646G>A) in the general population?

EMD p.Gly216Arg (c.646G>A) is rare (popmax 0.118%, afr) (gnomAD).

What do computational predictors say about EMD p.Gly216Arg (c.646G>A)?

AlphaMissense predicts likely benign (score 0.1866) — an in-silico prediction, not a clinical call.

EMD p.Gly216Arg

c.646G>A · rs147920229 · VCV42278

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 7 submitters

AlphaMissense

likely benign

0.1866 · ACMG-weighted

gnomAD v4.1

Rare

rare (popmax 0.118%, afr)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Cardiovascular phenotype

Computational evidence

Protein change
AlphaMissense	0.1866	likely benign
REVEL	0.192	benign-leaning
SaProt	LLR -6.38	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 3.3	GERP -0.57, phastCons 0.65
Regional constraint	o/e 1.05	unconstrained · MANE · 1,709 bp · p 0.47 · regional, not allelic
Overall
CADD	16.43	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.118% African / African-American · 68/57,515 alleles

Filtering AF 0.0956% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0874%

Overall 0.00644% 78/1,210,833 alleles · rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.118%	846
Remaining individualsnot grpmax-eligible	0.0168%	5,954
Admixed American	0.00218%	45,957
European (non-Finnish)	0.000112%	895,295

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.Gly216Arg
Coding: c.646G>A
MANE Select: NM_000117
dbSNP: rs147920229
Type: single nucleotide variant
Location: chrX:154381078 (GRCh38)
Structure: AlphaFold pLDDT 61.26 · 6 PDB
Residue 216: 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 Emery-Dreifuss muscular dystrophy 1, X-linked

Similar variants

EMD p.Gly216= Likely benign ★ 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
EMD c.399+1G>T Pathogenic ★★ same condition
EMD c.399+2T>C 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-gly216arg (accessed [today's date]).

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