CCL3L1 C-C motif chemokine ligand 3 like 1 [Homo sapiens (human)] - Gene

Summary

Official Symbol: CCL3L1provided by HGNC
Official Full Name: C-C motif chemokine ligand 3 like 1provided by HGNC
Primary source: HGNC:HGNC:10628
See related: MIM:601395; AllianceGenome:HGNC:10628
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: LD78; 464.2; MIP1AP; SCYA3L; G0S19-2; SCYA3L1; D17S1718; LD78BETA; LD78-beta(1-70)
Summary: This gene is one of several cytokine genes that are clustered on the q-arm of chromosome 17. Cytokines are a family of secreted proteins that function in inflammatory and immunoregulatory processes. The protein encoded by this gene binds to several chemokine receptors, including chemokine binding protein 2 and chemokine (C-C motif) receptor 5 (CCR5). CCR5 is a co-receptor for HIV, and binding of this protein to CCR5 inhibits HIV entry. The copy number of this gene varies among individuals, where most individuals have one to six copies, and a minority of individuals have zero or more than six copies. There are conflicting reports about copy number variation of this gene and its correlation to disease susceptibility. This record represents one of two copies that are present on the ALT_REF_LOCI_2 alternate haplotype of the GRCh38 human reference genome assembly. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, Apr 2014]
Annotation information: Annotation category: only annotated on alternate loci in reference assembly
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Genomic context

Location:: 17q21.1

Exon count:: 3

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	17 (ALT_REF_LOCI_2)	NT_187661.1 (250577..252466, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	17	NC_060941.1 (37368267..37370156, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	17	NC_000017.10 (34623842..34625731, complement)

NT_187661.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

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Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

CCL3L3-null status is associated with susceptibility to systemic lupus erythematosus.
Title: CCL3L3-null status is associated with susceptibility to systemic lupus erythematosus.
CCL3L1 high copy number variation is associated with HIV susceptibility.
Title: Population-specific profiling of CCL3L1 copy number of the three major ethnic groups in Malaysia and the implication on HIV susceptibility.
CCL3L1 and FCGR3B copy number variants may not be involved in susceptibility to ankylosing spondylitis risk in the Algerian population.
Title: Association study of copy number variants in CCL3L1, FCGR3A and FCGR3B genes with risk of ankylosing spondylitis in a West Algerian population.
We identified genes harboring CNVs that are highly differentiated between PM and global populations, indicating that these genes are predominantly enriched in immune responses and defense functions, including APOBEC3A_B, beta-defensin genes, and CCL3L1, followed by other biological functions, such as drug and toxin metabolism and responses to radiation
Title: A genome-wide characterization of copy number variations in native populations of Peninsular Malaysia.
Characterization of CCL3L1 CNVs with droplet digital PCR methodology highlighted specific CN genotypes in a French family sample. A copy number polymorphism of a rheumatoid arthritis (RA) candidate gene was quantified, and its significant association with RA was revealed in a Tunisian sample.
Title: Characterization of copy number variants for CCL3L1 gene in rheumatoid arthritis for French trio families and Tunisian cases and controls.
Studied copy number variation of the CCL3L1 gene in contributing to the host variation in susceptibility and response to HIV infection by analyzing a sub-Saharan African cohort.
Title: CCL3L1 copy number, HIV load, and immune reconstitution in sub-Saharan Africans.
no evidence for an influence of variation in genes coding for MIP-1alpha or CCR5 individually or together in susceptibility to clinically active TB
Title: CCL3L1 copy number, CCR5 genotype and susceptibility to tuberculosis.
Studies indicate beta-defensins (DEFB4, DEFB103, DEFB104), chemokine ligand 3 like 1 (CCL3L1), Fc gamma receptor 3B (FCGR3B), and complement component C4 (C4) for copy number variation in disease association.
Title: Correlating multiallelic copy number polymorphisms with disease susceptibility.
The number of CCL3L1 gene copies does not have a role in susceptibility to KD or CALs nor with IVIG resistance in Korean KD patients.
Title: Variations in the number of CCL3L1 gene copies and Kawasaki disease in Korean children.
The results do not support involvement of the CCL3L1 copy number variants in rheumatoid arthritis susceptibility.
Title: Association analysis of the CCL3L1 copy number locus by paralogue ratio test in Norwegian rheumatoid arthritis patients and healthy controls.

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Phenotypes

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Associated conditions

Description	Tests
Susceptibility to HIV infection MedGen: C1836230 OMIM: 609423 GeneReviews: Not available	Compare labs

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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Protein interactions

Protein	Gene	Interaction	Pubs
Envelope surface glycoprotein gp120	env	HIV-1 gp120-induced neuron death is inhibited by CCL3L1 treatment via the phosphorylation of CREB, the upregulation of Bcl-2, and the PKA and CaMKI/CaMKIV cell signaling pathways	PubMed
Envelope transmembrane glycoprotein gp41	env	A synthetic peptide corresponding to the immunosuppressive domain (amino acids 574-592) of HIV-1 gp41 upregulates the expression of chemokine (C-C motif) ligand 3-like 1 (CCL3L1) in peptide-treated PBMCs	PubMed
Nef	nef	HIV-1 Nef-stimulated CD8+ T cells upregulate mRNAs expression for IFN-gamma, MIP-1alpha, MIP-1alphaP, MIP-1beta, TNFRSF9, XCL1, and GM-CSF compared to unstimulated cells	PubMed
capsid	gag	HIV-1 CA-stimulated CD8+ T cells upregulate mRNAs expression for IFN-gamma, MIP-1alpha, MIP-1alphaP, MIP-1beta, TNFRSF9, XCL1, and GM-CSF compared to unstimulated cells	PubMed

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Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

SGC35233 (e-PCR)
- UniSTS:73603

RH68318 (e-PCR)
- UniSTS:35256

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables CCR chemokine receptor binding	IBA Inferred from Biological aspect of Ancestor more info
enables chemokine activity	IBA Inferred from Biological aspect of Ancestor more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in antimicrobial humoral immune response mediated by antimicrobial peptide	IBA Inferred from Biological aspect of Ancestor more info
involved_in cell chemotaxis	IBA Inferred from Biological aspect of Ancestor more info
involved_in chemokine-mediated signaling pathway	IBA Inferred from Biological aspect of Ancestor more info
involved_in inflammatory response	IBA Inferred from Biological aspect of Ancestor more info
involved_in inflammatory response	TAS Traceable Author Statement more info	PubMed
involved_in negative regulation of cell population proliferation	TAS Traceable Author Statement more info	PubMed
involved_in positive regulation of cell migration	IBA Inferred from Biological aspect of Ancestor more info

Component	Evidence Code	Pubs
located_in extracellular region	TAS Traceable Author Statement more info
is_active_in extracellular space	IBA Inferred from Biological aspect of Ancestor more info

General protein information

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Preferred Names: C-C motif chemokine 3-like 1

Names: G0/G1 switch regulatory protein 19-2; chemokine (C-C motif) ligand 3-like 1; small inducible cytokine A3-like 1; tonsillar lymphocyte LD78 beta protein

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

NG_023369.1 RefSeqGene

Range

5000..6889

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_021006.6 → NP_066286.1 C-C motif chemokine 3-like 1 precursor

See identical proteins and their annotated locations for NP_066286.1

Status: REVIEWED

Source sequence(s)

AC131056

UniProtKB/Swiss-Prot

A6NGK6, B2RUX4, P16619, Q3B7A8, Q53YA5, Q96I68

UniProtKB/TrEMBL

Q14745

Conserved Domains (1) summary

smart00199
Location:31 → 89

SCY; Intercrine alpha family (small cytokine C-X-C) (chemokine CXC)