EMD p.Val170=
c.510T>C · rs2148128835 · VCV1083510
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00235%, nfe)
Conditions
2
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 -1.8 | GERP -0.84 |
| Overall | ||
| CADD | 1.414 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00235%
European (non-Finnish) · 21/895,481 alleles
Filtering AF
0.00151%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00128%
Overall
0.00191%
21/1,098,034 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.Val170=
- Coding
- c.510T>C
- MANE Select
- NM_000117
- dbSNP
- rs2148128835
- Type
- single nucleotide variant
- Location
- chrX:154380942 (GRCh38)
- Structure
- AlphaFold pLDDT 61.26 · 6 PDB
- Residue 170
- the 'interaction with f-actin' region; the 'interaction with ctnnb1' region
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-val170 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown