CD58

CD58 molecule, the group of CD molecules|Ig-like cell adhesion molecule family|MicroRNA protein coding host genes

Basic information

Region (hg38): 1:116514533-116571039

Previous symbols: [ "LFA3" ]

Links

ENSG00000116815 ∙ NCBI:965 ∙ OMIM:153420 ∙ HGNC:1688 ∙ Uniprot:P19256 ∙ 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 CD58 gene.

• Inborn genetic diseases (8 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CD58 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	3		8
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	5	3	1

Variants in CD58

This is a list of pathogenic ClinVar variants found in the CD58 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-116514821-A-C		not specified	Uncertain significance (Aug 22, 2023)
1-116519238-T-C		not specified	Uncertain significance (Jan 06, 2023)
1-116521932-G-A		not specified	Likely benign (Nov 16, 2021)
1-116521970-G-C		not specified	Likely benign (Jun 09, 2022)
1-116535967-C-T		not specified	Uncertain significance (Aug 08, 2022)
1-116535977-T-C		not specified	Likely benign (Dec 19, 2022)
1-116536106-T-C		not specified	Uncertain significance (Aug 02, 2023)
1-116544347-T-C		not specified	Uncertain significance (Jun 30, 2022)
1-116544355-G-A		not specified	Uncertain significance (Nov 02, 2023)
1-116544574-T-C		not specified	Uncertain significance (Jan 05, 2022)
1-116558335-A-G			Benign (Jan 18, 2019)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CD58	protein_coding	protein_coding	ENST00000369489	6	56505

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.251	0.743	119138	0	1	119139	0.00000420

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.724	105	128	0.820	0.00000589	1630
Missense in Polyphen		15	31.673	0.47359		441
Synonymous	1.01	36	44.6	0.807	0.00000202	457
Loss of Function	2.39	3	11.9	0.253	5.64e-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	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00000939	0.00000939
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Ligand of the T-lymphocyte CD2 glycoprotein. This interaction is important in mediating thymocyte interactions with thymic epithelial cells, antigen-independent and -dependent interactions of T-lymphocytes with target cells and antigen- presenting cells and the T-lymphocyte rosetting with erythrocytes. In addition, the LFA-3/CD2 interaction may prime response by both the CD2+ and LFA-3+ cells.
• Pathway: Cell adhesion molecules (CAMs) - Homo sapiens (human);Epstein-Barr virus infection - Homo sapiens (human);Neutrophil degranulation;Innate Immune System;Immune System;Cell surface interactions at the vascular wall;Hemostasis (Consensus)

Recessive Scores

• pRec: 0.206

Intolerance Scores

• loftool: 0.479
• rvis_EVS: 0.62
• rvis_percentile_EVS: 83.14

Haploinsufficiency Scores

• pHI: 0.162
• hipred: N
• hipred_score: 0.145
• ghis: 0.431

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.453

Gene Damage Prediction

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

Gene ontology

• Biological process: heterotypic cell-cell adhesion;neutrophil degranulation;leukocyte migration;cellular response to interferon-gamma;cellular response to tumor necrosis factor;cell-cell adhesion;positive regulation of interleukin-8 secretion
• Cellular component: plasma membrane;integral component of plasma membrane;cell surface;membrane;secretory granule membrane;extracellular exosome;ficolin-1-rich granule membrane
• Molecular function: signaling receptor binding;protein binding