CD99
Basic information
Region (hg38): Y:2691187-2741309
Previous symbols: [ "MIC2", "MIC2X", "MIC2Y" ]
Links
Phenotypes
GenCC
Source:
Clinical Genomic Database
Source:
| Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
|---|---|---|---|---|---|
| XG blood group | BG | Hematologic | Variants associated with a blood group may be important in specific situations (eg, related to transfusion) | Hematologic | 22356523; 30061310 |
ClinVar
This is a list of variants' phenotypes submitted to
- not_provided (1 variants)
- CD99_Positive_Neoplastic_Cells_Present (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the CD99 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000002414.5. Only rare variants are included in the table.
In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.
Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 0 | |||||
| missense | 2 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 1 | 1 | 0 |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| CD99 | protein_coding | protein_coding | ENST00000381192 | 10 | 50131 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.00261 | 0.940 | 125580 | 0 | 10 | 125590 | 0.0000398 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | -0.529 | 129 | 113 | 1.14 | 0.00000659 | 1195 |
| Missense in Polyphen | 22 | 21.303 | 1.0327 | 231 | ||
| Synonymous | -0.164 | 44 | 42.6 | 1.03 | 0.00000275 | 354 |
| Loss of Function | 1.66 | 6 | 12.3 | 0.489 | 6.21e-7 | 141 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.000163 | 0.000163 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000617 | 0.0000617 |
| Middle Eastern | 0.000163 | 0.000163 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Involved in T-cell adhesion processes and in spontaneous rosette formation with erythrocytes. Plays a role in a late step of leukocyte extravasation helping leukocytes to overcome the endothelial basement membrane. Acts at the same site as, but independently of, PECAM1. Involved in T-cell adhesion processes (By similarity). {ECO:0000250}.;
- Pathway
- Cell adhesion molecules (CAMs) - Homo sapiens (human);Leukocyte transendothelial migration - Homo sapiens (human);Immune System;Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell;Adaptive Immune System;Cell surface interactions at the vascular wall;Hemostasis
(Consensus)
Recessive Scores
- pRec
- 0.287
Intolerance Scores
- loftool
- 0.711
- rvis_EVS
- 0.86
- rvis_percentile_EVS
- 88.62
Haploinsufficiency Scores
- pHI
- 0.119
- hipred
- N
- hipred_score
- 0.314
- ghis
- 0.417
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.916
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Gene ontology
- Biological process
- cell adhesion;regulation of immune response
- Cellular component
- cytoplasm;plasma membrane;integral component of plasma membrane;focal adhesion
- Molecular function
- protein binding