CD5

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

Basic information

Region (hg38): 11:61102489-61127852

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.

not_specified (51 variants)
not_provided (2 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. These statistics are base on transcript: NM_000014207.4. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous				1 clinvar		1
missense			50 clinvar	2 clinvar		52
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	50	3	0

Loading clinvar variants...

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