EMD p.Gln162=
c.486G>A · rs781879653 · VCV1743701
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00524%, afr)
Conditions
1
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 3.4 | GERP -0.71, phastCons 1 |
| Overall | ||
| CADD | 3.885 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00524%
African / African-American · 3/57,242 alleles
Filtering AF
0.00139%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000686%
Overall
0.000248%
3/1,210,104 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.Gln162=
- Coding
- c.486G>A
- MANE Select
- NM_000117
- dbSNP
- rs781879653
- Type
- single nucleotide variant
- Location
- chrX:154380918 (GRCh38)
- Structure
- AlphaFold pLDDT 61.26 · 6 PDB
- Residue 162
- the 'interaction with f-actin' region
Similar variants
- EMD p.Gln162Ter Pathogenic ★★ 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
- EMD p.Glu146Lys 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-gln162 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown