CD99
Chr YCD99 molecule (Xg blood group)
Also known as: HBA71, MIC2, MIC2X, MIC2Y, MSK5X
CD99 encodes a cell surface glycoprotein that mediates leukocyte migration across endothelial basement membranes and T-cell adhesion processes. Mutations cause 46,XY differences/disorders of sex development with gonadal dysgenesis, inherited in an X-linked pattern. The gene is located in the pseudoautosomal region and escapes X-inactivation, making it tolerant to loss-of-function variants.
Population Genetics & Constraint
gnomAD v4 — loss-of-function & missense intolerance
Typical tolerance to LoF variation
Tolerant to missense variation
This gene has evidence for multiple mechanisms of pathogenicity (dominant-negative and gain-of-function). Both the Badonyi & Marsh prediction and the broader genomic evidence point to dominant-negative as the predominant mechanism. Different variants in this gene may act through different mechanisms — interpret in context of the specific variant.
Note: In-silico variant effect predictors (SIFT, PolyPhen, REVEL, CADD) may underestimate pathogenicity of missense variants in genes with GOF or DN mechanisms. Consider functional evidence and clinical context.
Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312.
ClinVar Variant Classifications
200 submitted variants in ClinVar
Classification Summary
Curated Variants Distribution
Classified variants from ClinVar · 5 ACMG categories· variant type breakdown unavailable
| Classification | LoF | Missense + Inframe | Non-coding | Synonymous | Total |
|---|---|---|---|---|---|
Pathogenic | — | — | — | — | 25 |
Likely Pathogenic | — | — | — | — | 3 |
VUS | — | — | — | — | 2 |
Likely Benign | — | — | — | — | 2 |
Benign | — | — | — | — | 0 |
| Total | — | 32 | |||
Counts from ClinVar esearch · Updated hourly
View in ClinVar →Protein Context — Lollipop Plot
CD99 · protein map & ClinVar variants
Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.
3D Protein StructureAlphaFold
External Resources
Links to major genomics databases and tools
Clinical Trials
Active and recruiting trials from ClinicalTrials.gov
No active trials found for this gene.
Search ClinicalTrials.gov →External Resources
Links to major genomics databases and tools