CD99

CD99 molecule (Xg blood group), the group of CD molecules|Pseudoautosomal region 1|Blood group antigens

Basic information

Region (hg38): Y:2691187-2741309

Previous symbols: [ "MIC2", "MIC2X", "MIC2Y" ]

Links

∙ NCBI:4267 ∙ OMIM:313470, 450000 ∙ HGNC:7082 ∙ Uniprot:P14209 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

Clinical Genomic Database

Source: CGD

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 ClinVar and linked to the CD99 gene.

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.

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.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			2 clinvar	2 clinvar		4
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	2	2	0

Variants in CD99

This is a list of pathogenic ClinVar variants found in the CD99 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
Y-2720360-C-A			Likely benign (Feb 01, 2023)	2659860
Y-2740785-G-C		CD99 Positive Neoplastic Cells Present	Uncertain significance (Jan 01, 2019)	634582

GnomAD

Source: gnomAD

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: dbNSFP

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