CD80

CD80 molecule, the group of V-set domain containing|CD molecules|C2-set domain containing|B7 family

Basic information

Region (hg38): 3:119524292-119559614

Previous symbols: [ "CD28LG", "CD28LG1" ]

Links

ENSG00000121594 ∙ NCBI:941 ∙ OMIM:112203 ∙ HGNC:1700 ∙ Uniprot:P33681 ∙ 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 CD80 gene.

• Inborn genetic diseases (6 variants)
• not provided (4 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CD80 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	1
missense			6		1	7
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					2	2
Total	0	0	6	0	4

Variants in CD80

This is a list of pathogenic ClinVar variants found in the CD80 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-119525008-T-A			Benign (Feb 17, 2020)
3-119525574-A-C			Benign (Feb 17, 2020)
3-119527782-G-A		not specified	Uncertain significance (Jul 19, 2023)
3-119529857-A-G		not specified	Uncertain significance (Jun 01, 2023)
3-119537166-C-T		not specified	Uncertain significance (May 23, 2023)
3-119537173-G-A			Benign (Dec 31, 2019)
3-119537184-A-G		not specified	Uncertain significance (Oct 26, 2022)
3-119537397-A-G		not specified	Uncertain significance (Nov 08, 2022)
3-119544585-C-T		not specified	Uncertain significance (Oct 16, 2023)
3-119544671-G-C			Benign (Dec 31, 2019)
3-119544709-A-G		not specified	Uncertain significance (Apr 20, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CD80	protein_coding	protein_coding	ENST00000264246	5	35310

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0109	0.951	125724	0	11	125735	0.0000437

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.753	131	158	0.831	0.00000836	1890
Missense in Polyphen		33	48.746	0.67698		627
Synonymous	0.914	50	58.9	0.849	0.00000322	551
Loss of Function	1.80	5	11.6	0.429	4.89e-7	159

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.000163	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.0000529	0.0000527
Middle Eastern	0.000163	0.000163
South Asian	0.0000654	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in the costimulatory signal essential for T- lymphocyte activation. T-cell proliferation and cytokine production is induced by the binding of CD28, binding to CTLA-4 has opposite effects and inhibits T-cell activation. {ECO:0000269|PubMed:10583602}.
• Pathway: Cell adhesion molecules (CAMs) - Homo sapiens (human);Type I diabetes mellitus - Homo sapiens (human);Allograft rejection - Homo sapiens (human);Graft-versus-host disease - Homo sapiens (human);Viral myocarditis - Homo sapiens (human);Systemic lupus erythematosus - Homo sapiens (human);Autoimmune thyroid disease - Homo sapiens (human);Toll-like receptor signaling pathway - Homo sapiens (human);Rheumatoid arthritis - Homo sapiens (human);Intestinal immune network for IgA production - Homo sapiens (human);Regulation of toll-like receptor signaling pathway;Allograft Rejection;Primary Focal Segmental Glomerulosclerosis FSGS;Interleukin-10 signaling;PI3K-AKT-mTOR - VitD3 Signalling;Inflammatory Response Pathway;Toll-like Receptor Signaling Pathway;Disease;Signal Transduction;the co-stimulatory signal during t-cell activation;IL12 signaling mediated by STAT4;CD28 dependent PI3K/Akt signaling;CD28 dependent Vav1 pathway;CD28 co-stimulation;CTLA4 inhibitory signaling;Costimulation by the CD28 family;GPCR signaling-G alpha q;GPCR signaling-cholera toxin;GPCR signaling-pertussis toxin;TCR;Immune System;Adaptive Immune System;GPCR signaling-G alpha s Epac and ERK;GPCR signaling-G alpha s PKA and ERK;PIP3 activates AKT signaling;PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling;Negative regulation of the PI3K/AKT network;Constitutive Signaling by Aberrant PI3K in Cancer;PI3K/AKT Signaling in Cancer;GPCR signaling-G alpha i;Intracellular signaling by second messengers;Diseases of signal transduction;TCR signaling in naïve CD8+ T cells;TCR signaling in naïve CD4+ T cells;CD4 T cell receptor signaling-JNK cascade;CD4 T cell receptor signaling-NFkB cascade;CD4 T cell receptor signaling (Consensus)

Recessive Scores

• pRec: 0.634

Intolerance Scores

• loftool: 0.537
• rvis_EVS: 0.62
• rvis_percentile_EVS: 83.14

Haploinsufficiency Scores

• pHI: 0.0895
• hipred: N
• hipred_score: 0.132
• ghis: 0.480

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.554

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cd80
• Phenotype: cellular phenotype; endocrine/exocrine gland phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); immune system phenotype; hematopoietic system phenotype

Gene ontology

• Biological process: immune response;signal transduction;cell surface receptor signaling pathway;positive regulation of signal transduction;cytokine-mediated signaling pathway;T cell costimulation;intracellular signal transduction;positive regulation of T cell proliferation;negative regulation of T cell proliferation;positive regulation of interleukin-2 biosynthetic process;positive regulation of granulocyte macrophage colony-stimulating factor biosynthetic process;positive regulation of T-helper 1 cell differentiation;positive regulation of transcription, DNA-templated;viral entry into host cell;phosphatidylinositol phosphorylation;positive regulation of peptidyl-tyrosine phosphorylation;positive regulation of protein kinase B signaling;cellular response to lipopolysaccharide
• Cellular component: plasma membrane;external side of plasma membrane;cell surface;integral component of membrane;protein complex involved in cell adhesion
• Molecular function: virus receptor activity;protein binding;coreceptor activity;phosphatidylinositol-4,5-bisphosphate 3-kinase activity