EMC1 p.Ser569del
c.1703CCT[1] · rs1372501893 · VCV1364963
Uncertain significance
Multiple submitters
Classification
Uncertain significance
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0111%, eas)
Conditions
1
inherited retinal dystrophy
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 11 | GERP 2.2, phastCons 1 |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0111%
East Asian · 5/44,884 alleles
Filtering AF
0.00434%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00276%
Overall
0.000342%
5/1,461,888 alleles · ultra-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
- EMC1
- Protein
- p.Ser569del
- Coding
- c.1703CCT[1]
- MANE Select
- NM_015047
- dbSNP
- rs1372501893
- Type
- Microsatellite
- Location
- chr1:19232698 (GRCh38)
- Gene constraint
- LOEUF 0.913 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 87.67 · 10 PDB
- Residue 569
- a β-strand
Similar variants
- EMC1 p.Arg69Ter Pathogenic/Likely pathogenic ★★ same condition
- EMC1 p.Ala21Thr Uncertain significance ★★ ⚠ same condition
- EMC1 p.Arg275Gly Uncertain significance ★★ ⚠ same condition
- EMC1 p.Arg275Trp Uncertain significance ★★ ⚠ same condition
- EMC1 p.Arg288Trp Uncertain significance ★★ ⚠ same condition
- EMC1 p.Arg384Trp Uncertain significance ★★ ⚠ same condition
- EMC1 p.Arg802Cys Uncertain significance ★★ ⚠ same condition
- EMC1 p.Arg802His 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/emc1-p-ser569del (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown