CD99L2

CD99 molecule like 2

Basic information

Region (hg38): X:150766336-150898816

Previous symbols: [ "MIC2L1" ]

Links

ENSG00000102181 ∙ NCBI:83692 ∙ OMIM:300846 ∙ HGNC:18237 ∙ Uniprot:Q8TCZ2 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CD99L2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CD99L2 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				2	1	3
missense			19	4		23
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			1			1
Total	0	0	20	6	1

Variants in CD99L2

This is a list of pathogenic ClinVar variants found in the CD99L2 region.

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

Position	Type	Phenotype	Significance	ClinVar
X-150769039-T-C		not specified	Uncertain significance (Nov 09, 2024)
X-150769041-C-T			Likely benign (Aug 11, 2018)
X-150769049-T-G		not specified	Uncertain significance (Aug 01, 2024)
X-150769059-G-A		not specified	Uncertain significance (Sep 30, 2024)
X-150769064-C-T			Benign (May 14, 2018)
X-150769077-T-A		not specified	Uncertain significance (Oct 13, 2023)
X-150769091-G-A			Likely benign (Sep 01, 2022)
X-150769097-T-A			Uncertain significance (May 18, 2020)
X-150770310-G-A		not specified	Uncertain significance (Jun 26, 2024)
X-150770322-C-T		not specified	Uncertain significance (Oct 03, 2022)
X-150770325-C-T		not specified	Uncertain significance (Aug 17, 2022)
X-150770343-C-T		not specified	Uncertain significance (Nov 23, 2024)
X-150770349-C-T		not specified	Uncertain significance (Nov 10, 2024)
X-150770368-C-G		not specified	Uncertain significance (Jul 10, 2024)
X-150776225-C-T		not specified	Conflicting classifications of pathogenicity (Oct 25, 2024)
X-150776285-C-A		not specified	Uncertain significance (Nov 24, 2024)
X-150776287-A-G		not specified	Uncertain significance (Nov 09, 2024)
X-150777452-G-C		not specified	Uncertain significance (Mar 07, 2024)
X-150777456-C-T		Neurodevelopmental disorder	Benign/Likely benign (Jan 01, 2019)
X-150777461-T-C		not specified	Likely benign (Aug 12, 2021)
X-150777473-C-T		not specified	Uncertain significance (Nov 03, 2022)
X-150777474-G-A		not specified	Uncertain significance (Apr 01, 2024)
X-150793724-C-A		not specified	Uncertain significance (Jun 06, 2023)
X-150793736-C-G		not specified	Uncertain significance (Oct 27, 2023)
X-150795233-G-A		not specified	Uncertain significance (Nov 06, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CD99L2	protein_coding	protein_coding	ENST00000370377	11	132480

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000170	0.894	125719	9	16	125744	0.0000994

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.166	112	107	1.05	0.00000887	1689
Missense in Polyphen		33	37.834	0.87223		605
Synonymous	0.626	38	43.2	0.879	0.00000400	512
Loss of Function	1.47	8	13.9	0.575	0.00000130	188

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000113	0.0000988
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.000135	0.0000967
Middle Eastern	0.00	0.00
South Asian	0.000589	0.000359
Other	0.000221	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays a role in a late step of leukocyte extravasation helping cells to overcome the endothelial basement membrane. Acts at the same site as, but independently of, PECAM1 (By similarity). Homophilic adhesion molecule, but these interactions may not be required for cell aggregation (By similarity). {ECO:0000250}.
• Pathway: Cell surface interactions at the vascular wall;Hemostasis (Consensus)

Recessive Scores

• pRec: 0.0912

Intolerance Scores

• loftool: 0.391
• rvis_EVS: -0.27
• rvis_percentile_EVS: 34.32

Haploinsufficiency Scores

• pHI: 0.0761
• hipred: N
• hipred_score: 0.145
• ghis: 0.510

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 2.22e-16

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Cd99l2
• Phenotype: hematopoietic system phenotype; immune system phenotype; cellular phenotype

Gene ontology

• Biological process: cell adhesion;diapedesis;positive regulation of neutrophil extravasation;positive regulation of T cell extravasation
• Cellular component: plasma membrane;cell-cell adherens junction;focal adhesion;cell surface;integral component of membrane
• Molecular function: protein binding