CD93

protein-coding

CD93 molecule, the group of Complement system regulators and receptors|C-type lectin domain containing|CD molecules

Gene summary

The protein encoded by this gene is a cell-surface glycoprotein and type I membrane protein that was originally identified as a myeloid cell-specific marker. The encoded protein was once thought to be a receptor for C1q, but now is thought to instead be involved in intercellular adhesion and in the clearance of apoptotic cells. The intracellular cytoplasmic tail of this protein has been found to interact with moesin, a protein known to play a role in linking transmembrane proteins to the cytoskeleton and in the remodelling of the cytoskeleton. [provided by RefSeq, Jul 2008]

Previous symbols:

MXRA4
C1QR1

MANE transcript

NM_012072.4

Inheritance

—

ClinVar variants

U:117B:42

Top phenotype

CD93-related disorder

gnomAD constraint

pLI —, LoF o/e 0.82

Max pathogenic AF

—

Genomic locus

chr20:23,065,139-23,086,324

External References & Databases

Ensembl (ENSG00000125810)

Transcript & Mutation Effects

hg38 • Region Span ~21.2 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 CD93 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 146

CD93-related disorderTotal: 12

not providedTotal: 6

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_012072.4. 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			1 clinvar	22 clinvar	1 clinvar	24
missense			114 clinvar	17 clinvar	2 clinvar	133
nonsense			2 clinvar			2
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	117	39	3	159

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 7 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_012072.4	RefSeq	NP_036204.2	2	MANE Select
ENST00000246006.5	Ensembl	ENSP00000246006.4	2	MANE Select
ENST00000850633.1	Ensembl	ENSP00000520912.1	2	Standard
ENST00000850634.1	Ensembl	ENSP00000520913.1	2	Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / Model	Organism	Observed Phenotype
cd93	Danio rerio	Structure: epicardium Quality: increased size abnormal

Gene / Model

Organism

Observed Phenotype

cd93

Danio rerio

Structure: epicardium

Quality: increased size

abnormal

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Human Complement System
Neutrophil degranulation
Innate Immune System
Immune System

Biological Process

phagocytosis
viral process
macrophage activation
neutrophil degranulation
cell-cell adhesion

Molecular Function

complement component C1q binding
calcium ion binding
protein binding
carbohydrate binding
signaling receptor activity

Cellular Component

plasma membrane
cell surface
integral component of membrane
secretory granule membrane
specific granule membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000246006
Coding exons: 2
Length: 6992
Individuals with no LoFs: 125698
Homozygous LoFs: 0
Heterozygous LoFs: 50
Defined: 125748
p: 0.000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.351	413	393	1.05	0.0000238	4158
Missense (PolyPhen)		119	122.56	0.97098		1473
Synonymous	-1.38	209	185	1.13	0.0000126	1396
Loss of Function	0.743	17	20.6	0.824	0.00000121	207

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00031	0.00031	rare
Latino/Admixed American	0.000091	0.000087	rare
Ashkenazi Jewish	0.00010	0.000099	rare
East Asian	0.00018	0.00016	rare
Finnish	0.000047	0.000046	rare
European (Non-Finnish)	0.00023	0.00022	rare
South Asian	0.00033	0.00033	rare
Other	0.00033	0.00033	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Receptor (or element of a larger receptor complex) for C1q, mannose-binding lectin (MBL2) and pulmonary surfactant protein A (SPA). May mediate the enhancement of phagocytosis in monocytes and macrophages upon interaction with soluble defense collagens. May play a role in intercellular adhesion.;

Recessive Scores

pRec: 0.288

Intolerance Scores

LoFtool: 0.265
RVIS EVS: -0.15
RVIS percentile EVS: 42.3

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.729

Gene Damage Prediction

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