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

ENSG00000110448NCBI:921OMIM:153340HGNC:1685Uniprot:P06127AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

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.

EffectPLPVUSLBBSum
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

GeneTypeBio TypeTranscript Coding Exons Length
CD5protein_codingprotein_codingENST00000347785 1025458
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
2.31e-100.6731257031441257480.000179
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.9622412870.8400.00001703199
Missense in Polyphen7592.4020.811671025
Synonymous0.3151171210.9640.00000752992
Loss of Function1.441927.10.7020.00000139287

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0001260.000124
Ashkenazi Jewish0.000.00
East Asian0.0002180.000217
Finnish0.00009530.0000924
European (Non-Finnish)0.0002130.000211
Middle Eastern0.0002180.000217
South Asian0.0003950.000359
Other0.0001640.000163

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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