CD99 p.Asp66Glu
c.198C>A · rs1230661797 · VCV2659860
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00534%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.038 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -0.64 | GERP 2.2 |
| Regional constraint | o/e 1.14 | unconstrained · MANE · 49 kb · p 0.03 · regional, not allelic |
| Overall | ||
| CADD | 8.524 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00534%
African / African-American · 4/74,840 alleles
Filtering AF
0.00175%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00104%
Overall
0.00031%
5/1,613,626 alleles · very rare
exomes 4/1,461,638 · genomes 1/151,988 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.00534% | 18,710 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,456 |
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
- CD99
- Protein
- p.Asp66Glu
- Coding
- c.198C>A
- MANE Select
- NM_002414
- dbSNP
- rs1230661797
- Type
- single nucleotide variant
- Location
- chrX:2720360 (GRCh38)
- Structure
- AlphaFold pLDDT 60.43 · 1 PDB
- Residue 66
- the 'disordered' region
Similar variants
- CD99 p.Arg180Pro Uncertain significance ★ 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/cd99-p-asp66glu (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown