CD5

CD5 molecule, the group of CD molecules|Scavenger receptor cysteine rich domain containing

Basic information

Region (hg38): 11:61102488-61127852

Previous symbols: [ "LEU1" ]

Links

ENSG00000110448 ∙ NCBI:921 ∙ OMIM:153340 ∙ HGNC:1685 ∙ Uniprot:P06127 ∙ 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 CD5 gene.

• Inborn genetic diseases (21 variants)
• not provided (4 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CD5 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			21	1	2	24
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	21	2	2

Variants in CD5

This is a list of pathogenic ClinVar variants found in the CD5 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-61118195-C-T		not specified	Uncertain significance (Oct 12, 2022)
11-61118205-C-T		not specified	Uncertain significance (Nov 21, 2023)
11-61118243-G-A		not specified	Uncertain significance (Sep 15, 2021)
11-61118253-T-A		not specified	Uncertain significance (Jul 21, 2021)
11-61118282-T-G		not specified	Uncertain significance (Aug 02, 2021)
11-61118327-C-T		not specified	Uncertain significance (Jun 14, 2023)
11-61118381-C-G		not specified	Uncertain significance (Jan 26, 2023)
11-61118381-C-T		not specified	Uncertain significance (Aug 22, 2023)
11-61118951-C-T		not specified	Uncertain significance (Jul 14, 2021)
11-61118960-C-A		not specified	Uncertain significance (Dec 20, 2023)
11-61119287-G-A		not specified	Uncertain significance (Oct 27, 2022)
11-61119289-G-T			Likely benign (Oct 01, 2022)
11-61119441-C-T			Benign (Jan 18, 2019)
11-61119474-T-C		not specified	Uncertain significance (Feb 16, 2023)
11-61119493-C-G		not specified	Uncertain significance (Oct 12, 2021)
11-61119563-C-G		not specified	Uncertain significance (Mar 22, 2023)
11-61121647-G-A		not specified	Uncertain significance (Jun 29, 2023)
11-61121653-G-C		not specified	Uncertain significance (Dec 09, 2023)
11-61121673-G-A		not specified	Uncertain significance (Sep 01, 2021)
11-61121788-G-A		not specified	Likely benign (Apr 04, 2023)
11-61121818-G-A		not specified	Uncertain significance (Oct 27, 2021)
11-61122915-C-G			Uncertain significance (Nov 23, 2021)
11-61122975-C-G		not specified	Uncertain significance (Dec 27, 2023)
11-61123902-G-A		not specified	Uncertain significance (Aug 10, 2021)
11-61125044-G-A		not specified	Uncertain significance (Feb 06, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CD5	protein_coding	protein_coding	ENST00000347785	10	25458

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.31e-10	0.673	125703	1	44	125748	0.000179

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.962	241	287	0.840	0.0000170	3199
Missense in Polyphen		75	92.402	0.81167		1025
Synonymous	0.315	117	121	0.964	0.00000752	992
Loss of Function	1.44	19	27.1	0.702	0.00000139	287

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000126	0.000124
Ashkenazi Jewish	0.00	0.00
East Asian	0.000218	0.000217
Finnish	0.0000953	0.0000924
European (Non-Finnish)	0.000213	0.000211
Middle Eastern	0.000218	0.000217
South Asian	0.000395	0.000359
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May act as a receptor in regulating T-cell proliferation.
• Pathway: Hematopoietic cell lineage - Homo sapiens (human);TCR;BCR (Consensus)

Recessive Scores

• pRec: 0.467

Intolerance Scores

• loftool: 0.701
• rvis_EVS: 0.8
• rvis_percentile_EVS: 87.66

Haploinsufficiency Scores

• pHI: 0.177
• hipred: N
• hipred_score: 0.406
• ghis: 0.402

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.667

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cd5
• Phenotype: integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); immune system phenotype; hematopoietic system phenotype; normal 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)

Gene ontology

• Biological process: receptor-mediated endocytosis;cell recognition;cell population proliferation;T cell costimulation;apoptotic signaling pathway
• Cellular component: plasma membrane;integral component of plasma membrane;external side of plasma membrane
• Molecular function: transmembrane signaling receptor activity;scavenger receptor activity;protein binding;signaling receptor activity