CD99L2

protein-coding

CD99 molecule like 2

Gene summary

This gene encodes a cell-surface protein that is similar to CD99. A similar protein in mouse functions as an adhesion molecule during leukocyte extravasation. Alternate splicing results in multiple transcript variants. [provided by RefSeq, May 2010]

Previous symbols:

MIC2L1

MANE transcript

NM_031462.4

Inheritance

—

ClinVar variants

U:105B:8

Top phenotype

Neurodevelopmental disorder

gnomAD constraint

pLI —, LoF o/e 0.57

Max pathogenic AF

—

Genomic locus

chrX:150,766,336-150,898,816

External References & Databases

Ensembl (ENSG00000102181)

Transcript & Mutation Effects

hg38 • Region Span ~132.5 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to CD99L2 variants in ClinVar

4 Conditions Cataloged

not specifiedTotal: 48

not providedTotal: 7

Neurodevelopmental disorderTotal: 1

Inclusion body myositisTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_031462.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			12 clinvar	2 clinvar	1 clinvar	15
missense			64 clinvar	5 clinvar		69
nonsense			3 clinvar			3
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			26 clinvar			26
Total	0	0	105	7	1	113

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 66 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_031462.4	RefSeq	NP_113650.2	11	MANE Select
ENST00000370377.8	Ensembl	ENSP00000359403.3	11	MANE Select
NM_001184808.2	RefSeq	NP_001171737.1	8	Standard
NM_001242614.2	RefSeq	NP_001229543.1	12	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Cell surface interactions at the vascular wall
Hemostasis

Biological Process

cell adhesion
diapedesis
positive regulation of neutrophil extravasation
positive regulation of T cell extravasation

Molecular Function

protein binding

Cellular Component

plasma membrane
cell-cell adherens junction
focal adhesion
cell surface
integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000370377
Coding exons: 11
Length: 132480
Individuals with no LoFs: 125719
Homozygous LoFs: 9
Heterozygous LoFs: 16
Defined: 125744
p: 0.0000994

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.166	112	107	1.05	0.00000887	1689
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000076	0.000062	rare
Latino/Admixed American	0.000037	0.000029	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.00014	0.000097	rare
South Asian	0.00059	0.00036	rare
Other	0.00022	0.00016	rare

dbNSFP Gene Annotations

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}.;

Recessive Scores

pRec: 0.0912

Intolerance Scores

LoFtool: 0.391
RVIS EVS: -0.27
RVIS percentile EVS: 34.32

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 2.22e-16

Gene Damage Prediction

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