CD53

CD53 molecule, the group of Tetraspanins|CD molecules

Basic information

Region (hg38): 1:110871187-110899922

Previous symbols: [ "MOX44" ]

Links

ENSG00000143119 ∙ NCBI:963 ∙ OMIM:151525 ∙ HGNC:1686 ∙ Uniprot:P19397 ∙ 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 CD53 gene.

• Inborn genetic diseases (5 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CD53 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			5			5
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	5	0	0

Variants in CD53

This is a list of pathogenic ClinVar variants found in the CD53 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-110892415-A-G		not specified	Uncertain significance (Sep 12, 2023)
1-110892444-G-A		not specified	Uncertain significance (Jul 12, 2022)
1-110895003-G-A		not specified	Uncertain significance (Jun 28, 2022)
1-110896653-C-G		not specified	Uncertain significance (Jul 26, 2021)
1-110896707-T-C		not specified	Uncertain significance (Jan 18, 2023)
1-110897857-A-G		not specified	Uncertain significance (Mar 16, 2022)
1-110897873-T-C		not specified	Uncertain significance (Jul 11, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CD53	protein_coding	protein_coding	ENST00000271324	7	26776

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00230	0.930	125731	0	16	125747	0.0000636

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.810	96	121	0.793	0.00000614	1437
Missense in Polyphen		28	43.095	0.64972		546
Synonymous	-0.453	55	50.9	1.08	0.00000280	424
Loss of Function	1.60	6	12.0	0.502	5.72e-7	138

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000580	0.0000580
Ashkenazi Jewish	0.0000998	0.0000992
East Asian	0.0000544	0.0000544
Finnish	0.000185	0.000185
European (Non-Finnish)	0.0000616	0.0000615
Middle Eastern	0.0000544	0.0000544
South Asian	0.00	0.00
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Required for efficient formation of myofibers in regenerating muscle at the level of cell fusion. May be involved in growth regulation in hematopoietic cells (By similarity). {ECO:0000250}.
• Pathway: Neutrophil degranulation;Innate Immune System;Immune System (Consensus)

Recessive Scores

• pRec: 0.219

Intolerance Scores

• loftool: 0.518
• rvis_EVS: -0.21
• rvis_percentile_EVS: 38.28

Haploinsufficiency Scores

• pHI: 0.339
• hipred: N
• hipred_score: 0.324
• ghis: 0.636

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.873

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cd53
• Phenotype: hematopoietic system phenotype; immune system phenotype

Gene ontology

• Biological process: signal transduction;cell surface receptor signaling pathway;neutrophil degranulation;positive regulation of myoblast fusion
• Cellular component: immunological synapse;plasma membrane;integral component of plasma membrane;cell-cell junction;specific granule membrane;extracellular exosome;tertiary granule membrane
• Molecular function: protein binding