CD93

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

Basic information

Region (hg38): 20:23065139-23086324

Previous symbols: [ "MXRA4", "C1QR1" ]

Links

ENSG00000125810 ∙ NCBI:22918 ∙ OMIM:120577 ∙ HGNC:15855 ∙ Uniprot:Q9NPY3 ∙ 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 CD93 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CD93 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	2	4
missense			31	2	5	38
nonsense			1			1
start loss						0
frameshift						0
inframe indel				1		1
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	32	5	8

Variants in CD93

This is a list of pathogenic ClinVar variants found in the CD93 region.

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

Position	Type	Phenotype	Significance	ClinVar
20-23083972-G-A		not specified	Uncertain significance (Feb 13, 2023)
20-23084173-C-T		not specified	Benign (Jan 24, 2024)
20-23084267-G-T		not specified	Uncertain significance (Mar 20, 2024)
20-23084292-C-T		not specified	Uncertain significance (Jan 17, 2023)
20-23084293-G-A		CD93-related disorder	Uncertain significance (May 05, 2023)
20-23084337-T-G		not specified	Uncertain significance (Aug 17, 2022)
20-23084355-C-T		not specified	Uncertain significance (Dec 04, 2023)
20-23084361-G-C		not specified	Uncertain significance (Sep 30, 2021)
20-23084368-G-A		not specified	Uncertain significance (Mar 15, 2024)
20-23084373-C-T		not specified	Uncertain significance (Dec 12, 2023)
20-23084416-T-C		not specified	Uncertain significance (Nov 08, 2022)
20-23084442-A-T		not specified	Uncertain significance (Jun 27, 2023)
20-23084566-C-T		CD93-related disorder	Likely benign (Feb 28, 2023)
20-23084572-G-A		not specified	Benign (Jan 24, 2024)
20-23084584-G-A		not specified	Uncertain significance (Oct 26, 2021)
20-23084634-G-A			Benign (Dec 31, 2019)
20-23084646-G-C		not specified	Uncertain significance (May 05, 2023)
20-23084692-T-C		not specified	Uncertain significance (Mar 18, 2024)
20-23084705-A-G		not specified	Benign (Jan 24, 2024)
20-23084706-C-T		CD93-related disorder	Likely benign (Apr 12, 2022)
20-23084707-G-A		CD93-related disorder	Likely benign (Apr 11, 2024)
20-23084710-G-A		not specified	Uncertain significance (Feb 13, 2024)
20-23084715-G-A			Benign (Jul 23, 2018)
20-23084738-GTCC-G		CD93-related disorder	Likely benign (Nov 27, 2023)
20-23084754-G-C		CD93-related disorder	Uncertain significance (Dec 05, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CD93	protein_coding	protein_coding	ENST00000246006	2	6992

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.98e-10	0.235	125698	0	50	125748	0.000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.351	413	393	1.05	0.0000238	4158
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000400	0.000398
Ashkenazi Jewish	0.000105	0.0000992
East Asian	0.000176	0.000163
Finnish	0.0000474	0.0000462
European (Non-Finnish)	0.000228	0.000220
Middle Eastern	0.000176	0.000163
South Asian	0.000328	0.000327
Other	0.000327	0.000326

dbNSFP

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.
• Pathway: Human Complement System;Neutrophil degranulation;Innate Immune System;Immune System (Consensus)

Recessive Scores

• pRec: 0.288

Intolerance Scores

• loftool: 0.265
• rvis_EVS: -0.15
• rvis_percentile_EVS: 42.3

Haploinsufficiency Scores

• pHI: 0.155
• hipred: N
• hipred_score: 0.173
• ghis: 0.521

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.729

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cd93
• Phenotype: hematopoietic system phenotype; immune system phenotype

Zebrafish Information Network

• Gene name: cd93
• Affected structure: epicardium
• Phenotype tag: abnormal
• Phenotype quality: increased size

Gene ontology

• Biological process: phagocytosis;viral process;macrophage activation;neutrophil degranulation;cell-cell adhesion
• Cellular component: plasma membrane;cell surface;integral component of membrane;secretory granule membrane;specific granule membrane;tertiary granule membrane;ficolin-1-rich granule membrane
• Molecular function: complement component C1q binding;calcium ion binding;protein binding;carbohydrate binding;signaling receptor activity