CD93 p.Glu484del
c.1449GGA[1] · rs556056799 · VCV3044385
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.2%, mid)
Conditions
1
CD93-related disorder
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 -0.53 | GERP -3.4 |
| Overall | ||
| CADD | 0.74 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.2%
Middle Eastern · 12/6,004 alleles
Filtering AF
0.126%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.116%
Overall
0.0334%
536/1,607,004 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.2% | 500 |
| Admixed American | 0.151% | 662 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0967% | 1,034 |
| Remaining individualsnot grpmax-eligible | 0.0676% | 1,479 |
| South Asian | 0.0365% | 2,736 |
| European (non-Finnish) | 0.0275% | 3,633 |
| African / African-American | 0.00937% | 10,673 |
| Finnishnot grpmax-eligible | 0.00159% | 63,054 |
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
- CD93
- Protein
- p.Glu484del
- Coding
- c.1449GGA[1]
- MANE Select
- NM_012072
- dbSNP
- rs556056799
- Type
- Microsatellite
- Location
- chr20:23084739 (GRCh38)
- Gene constraint
- LOEUF 1.237 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 73.07 · 2 PDB
- Residue 484
- the 'disordered' region
Disease context
CD93-related disorder
Similar variants
- CD93 p.Arg634Ter Uncertain significance ★ same condition
- CD93 p.Met187Ile Uncertain significance ⚠ same condition
- CD93 p.Arg496Cys Likely benign ⚠ same condition
- CD93 p.Arg496His Likely benign same condition
- CD93 p.Ser41= Likely benign same condition
- CD93 p.Val117Gly Benign ⚠ same condition
- CD93 p.Leu15del Likely benign ★ same type
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/cd93-p-glu484del (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown