CD163

CD163 molecule, the group of CD molecules|Scavenger receptor cysteine rich domain containing|Scavenger receptors

Basic information

Region (hg38): 12:7470811-7503893

Links

ENSG00000177575 ∙ NCBI:9332 ∙ OMIM:605545 ∙ HGNC:1631 ∙ Uniprot:Q86VB7 ∙ 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 CD163 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CD163 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				1	5	6
missense			44	4	4	52
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region			1			1
non coding			2		1	3
Total	0	0	46	5	10

Variants in CD163

This is a list of pathogenic ClinVar variants found in the CD163 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-7479937-G-T			Benign (Aug 16, 2018)
12-7479969-C-T			Likely benign (Feb 26, 2018)
12-7480057-G-C		Lung adenocarcinoma	Uncertain significance (Jun 06, 2022)
12-7482667-G-A		Multisystem inflammatory syndrome in children	risk factor (Nov 14, 2021)
12-7482683-G-T		not specified	Likely benign (Jan 16, 2024)
12-7482712-C-T		not specified	Likely benign (Feb 21, 2024)
12-7482733-C-T		not specified	Uncertain significance (Mar 29, 2023)
12-7482750-C-T		not specified	Uncertain significance (Dec 06, 2021)
12-7482756-G-A		not specified	Uncertain significance (Aug 30, 2022)
12-7482972-T-G		not specified	Uncertain significance (Apr 03, 2023)
12-7483431-A-G			Benign (Feb 26, 2018)
12-7483460-T-G		not specified	Uncertain significance (Jan 02, 2024)
12-7483474-T-C		not specified	Uncertain significance (Aug 23, 2021)
12-7483666-C-A		not specified	Uncertain significance (May 20, 2024)
12-7485112-G-A			Benign (Dec 13, 2017)
12-7485122-G-A		not specified	Uncertain significance (Aug 02, 2021)
12-7485176-T-G		not specified	Uncertain significance (Mar 07, 2023)
12-7485199-A-G			Benign (May 14, 2018)
12-7485276-G-A			Benign (Jul 31, 2018)
12-7485306-C-T		not specified	Uncertain significance (Jun 24, 2022)
12-7485410-A-G		not specified	Uncertain significance (May 23, 2024)
12-7486553-C-T		not specified	Uncertain significance (May 10, 2024)
12-7486577-G-C		not specified	Uncertain significance (Aug 02, 2021)
12-7486588-C-T		not specified	Uncertain significance (Mar 28, 2024)
12-7486603-T-C		not specified	Uncertain significance (Jun 16, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CD163	protein_coding	protein_coding	ENST00000359156	16	33081

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000834	0.999	125699	0	44	125743	0.000175

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.51	455	633	0.719	0.0000329	7537
Missense in Polyphen		137	251.76	0.54417		3081
Synonymous	0.335	221	227	0.972	0.0000123	2227
Loss of Function	4.95	17	57.6	0.295	0.00000262	696

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000499	0.000499
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.000212	0.000211
Middle Eastern	0.000109	0.000109
South Asian	0.000196	0.000196
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Acute phase-regulated receptor involved in clearance and endocytosis of hemoglobin/haptoglobin complexes by macrophages and may thereby protect tissues from free hemoglobin-mediated oxidative damage. May play a role in the uptake and recycling of iron, via endocytosis of hemoglobin/haptoglobin and subsequent breakdown of heme. Binds hemoglobin/haptoglobin complexes in a calcium-dependent and pH-dependent manner. Exhibits a higher affinity for complexes of hemoglobin and multimeric haptoglobin of HP*1F phenotype than for complexes of hemoglobin and dimeric haptoglobin of HP*1S phenotype. Induces a cascade of intracellular signals that involves tyrosine kinase-dependent calcium mobilization, inositol triphosphate production and secretion of IL6 and CSF1. Isoform 3 exhibits the higher capacity for ligand endocytosis and the more pronounced surface expression when expressed in cells.
• Pathway: Macrophage markers;Protein alkylation leading to liver fibrosis;Macrophage markers;TWEAK;Vesicle-mediated transport;Scavenging of heme from plasma;Binding and Uptake of Ligands by Scavenger Receptors (Consensus)

Recessive Scores

• pRec: 0.234

Intolerance Scores

• rvis_EVS: -0.11
• rvis_percentile_EVS: 45.61

Haploinsufficiency Scores

• pHI: 0.227
• hipred: N
• hipred_score: 0.332
• ghis: 0.465

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.131

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cd163
• Phenotype: hematopoietic system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); respiratory system phenotype; immune system phenotype; vision/eye phenotype; homeostasis/metabolism phenotype; cellular phenotype; muscle phenotype

Gene ontology

• Biological process: receptor-mediated endocytosis;acute-phase response
• Cellular component: extracellular region;plasma membrane;integral component of plasma membrane;external side of plasma membrane;endocytic vesicle membrane
• Molecular function: scavenger receptor activity;protein binding