Is EMD p.Gly24= (c.72G>T) pathogenic?

EMD p.Gly24= (c.72G>T) is classified Likely benign in EMD (ClinVar, Single submitter, 1 submitter; last evaluated 2022-06-22). Absent from gnomAD v4.1; Associated with Cardiovascular phenotype.

What condition is associated with EMD p.Gly24= (c.72G>T)?

EMD p.Gly24= (c.72G>T) is associated with Cardiovascular phenotype (ClinVar).

How common is EMD p.Gly24= (c.72G>T) in the general population?

EMD p.Gly24= (c.72G>T) is absent from gnomAD v4.1 (gnomAD).

EMD p.Gly24=

c.72G>T · rs2522787142 · VCV1758206

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,170,266)

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 2.2	GERP -1.1, phastCons 1
Overall
CADD	8.811	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

No allele count reported in gnomAD v4.1 (AN 1,170,266). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: EMD
Protein: p.Gly24=
Coding: c.72G>T
MANE Select: NM_000117
dbSNP: rs2522787142
Type: single nucleotide variant
Location: chrX:154379556 (GRCh38)
Structure: AlphaFold pLDDT 61.26 · 6 PDB
Residue 24: the lem domain

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

Similar variants

EMD p.Gly24Arg Uncertain significance ★★ ⚠ same residue
EMD p.Gly24Val Uncertain significance ★ ⚠ same residue
EMD c.400-3C>T Uncertain significance ★★ same condition
EMD c.449+4C>T Uncertain significance ★★ same condition
EMD p.Arg168Cys Uncertain significance ★★ ⚠ same condition
EMD p.Arg203His Uncertain significance ★★ ⚠ same condition
EMD p.Arg207Gln Uncertain significance ★★ ⚠ same condition
EMD p.Asp72Val Uncertain significance ★★ ⚠ 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-gly24 (accessed [today's date]).

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