CD5L

CD5 molecule like, the group of Scavenger receptor cysteine rich domain containing

Basic information

Region (hg38): 1:157830911-157898256

Previous symbols: [ "API6" ]

Links

ENSG00000073754 ∙ NCBI:922 ∙ OMIM:602592 ∙ HGNC:1690 ∙ Uniprot:O43866 ∙ 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 CD5L gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CD5L 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			23	1		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	23	1	0

Variants in CD5L

This is a list of pathogenic ClinVar variants found in the CD5L region.

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

Position	Type	Phenotype	Significance	ClinVar
1-157833248-C-A		not specified	Uncertain significance (Jul 13, 2022)
1-157833261-G-T		not specified	Uncertain significance (Aug 05, 2024)
1-157833278-T-C		not specified	Uncertain significance (Mar 10, 2025)
1-157833318-C-T		not specified	Uncertain significance (Nov 14, 2023)
1-157833320-C-A		not specified	Uncertain significance (Feb 13, 2025)
1-157833354-G-A		not specified	Uncertain significance (Mar 13, 2023)
1-157833432-A-C		not specified	Uncertain significance (Mar 28, 2023)
1-157833447-T-C		not specified	Uncertain significance (Jan 23, 2024)
1-157834408-T-G		not specified	Uncertain significance (Sep 22, 2021)
1-157834416-C-T		not specified	Uncertain significance (Mar 14, 2025)
1-157834511-T-C		not specified	Uncertain significance (Jun 05, 2023)
1-157834513-G-C		not specified	Uncertain significance (Aug 21, 2023)
1-157834554-A-G		not specified	Uncertain significance (Jul 26, 2022)
1-157834611-C-A		not specified	Uncertain significance (Aug 03, 2022)
1-157834616-C-T		not specified	Likely benign (Aug 12, 2024)
1-157834644-T-C		not specified	Uncertain significance (Oct 06, 2024)
1-157834676-C-A		not specified	Uncertain significance (Jun 22, 2021)
1-157835886-C-G		not specified	Uncertain significance (Oct 26, 2021)
1-157835915-G-T		not specified	Uncertain significance (Dec 30, 2023)
1-157835951-T-C		not specified	Uncertain significance (Feb 25, 2025)
1-157835961-C-G		not specified	Uncertain significance (Dec 12, 2023)
1-157835975-T-C		not specified	Uncertain significance (Jan 08, 2024)
1-157835997-C-T		not specified	Uncertain significance (Oct 06, 2024)
1-157836035-G-A		not specified	Uncertain significance (Feb 28, 2024)
1-157836051-C-A		not specified	Uncertain significance (May 05, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CD5L	protein_coding	protein_coding	ENST00000368174	6	67343

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.23e-17	0.00157	125122	3	623	125748	0.00249

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0595	200	202	0.988	0.0000120	2234
Missense in Polyphen		76	74.22	1.024		853
Synonymous	-0.544	87	80.8	1.08	0.00000475	687
Loss of Function	-0.752	23	19.4	1.18	0.00000108	208

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00227	0.00227
Ashkenazi Jewish	0.000199	0.000198
East Asian	0.000435	0.000435
Finnish	0.000323	0.000323
European (Non-Finnish)	0.00291	0.00290
Middle Eastern	0.000435	0.000435
South Asian	0.00677	0.00672
Other	0.00179	0.00179

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Secreted protein that acts as a key regulator of lipid synthesis: mainly expressed by macrophages in lymphoid and inflammed tissues and regulates mechanisms in inflammatory responses, such as infection or atherosclerosis. Able to inhibit lipid droplet size in adipocytes. Following incorporation into mature adipocytes via CD36-mediated endocytosis, associates with cytosolic FASN, inhibiting fatty acid synthase activity and leading to lipolysis, the degradation of triacylglycerols into glycerol and free fatty acids (FFA). CD5L-induced lipolysis occurs with progression of obesity: participates in obesity-associated inflammation following recruitment of inflammatory macrophages into adipose tissues, a cause of insulin resistance and obesity- related metabolic disease. Regulation of intracellular lipids mediated by CD5L has a direct effect on transcription regulation mediated by nuclear receptors ROR-gamma (RORC). Acts as a key regulator of metabolic switch in T-helper Th17 cells. Regulates the expression of pro-inflammatory genes in Th17 cells by altering the lipid content and limiting synthesis of cholesterol ligand of RORC, the master transcription factor of Th17-cell differentiation. CD5L is mainly present in non-pathogenic Th17 cells, where it decreases the content of polyunsaturated fatty acyls (PUFA), affecting two metabolic proteins MSMO1 and CYP51A1, which synthesize ligands of RORC, limiting RORC activity and expression of pro-inflammatory genes. Participates in obesity- associated autoimmunity via its association with IgM, interfering with the binding of IgM to Fcalpha/mu receptor and enhancing the development of long-lived plasma cells that produce high-affinity IgG autoantibodies (By similarity). Also acts as an inhibitor of apoptosis in macrophages: promotes macrophage survival from the apoptotic effects of oxidized lipids in case of atherosclerosis (PubMed:24295828). Involved in early response to microbial infection against various pathogens by acting as a pattern recognition receptor and by promoting autophagy (PubMed:16030018, PubMed:24223991, PubMed:24583716, PubMed:25713983). {ECO:0000250|UniProtKB:Q9QWK4, ECO:0000269|PubMed:16030018, ECO:0000269|PubMed:24223991, ECO:0000269|PubMed:24295828, ECO:0000269|PubMed:24583716, ECO:0000269|PubMed:25713983}.

Recessive Scores

• pRec: 0.253

Intolerance Scores

• loftool: 0.624
• rvis_EVS: 0.33
• rvis_percentile_EVS: 73.41

Haploinsufficiency Scores

• pHI: 0.0527
• hipred: N
• hipred_score: 0.123

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0983

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cd5l
• Phenotype: immune system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); hematopoietic system phenotype; endocrine/exocrine gland 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)

Gene ontology

• Biological process: immune system process;receptor-mediated endocytosis;apoptotic process;inflammatory response;cellular defense response
• Cellular component: extracellular region;extracellular space;cytoplasm;membrane;blood microparticle
• Molecular function: scavenger receptor activity