CCL28

C-C motif chemokine ligand 28, the group of Chemokine ligands

Basic information

Region (hg38): 5:43376645-43412391

Links

ENSG00000151882 ∙ NCBI:56477 ∙ OMIM:605240 ∙ HGNC:17700 ∙ Uniprot:Q9NRJ3 ∙ 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 CCL28 gene.

• not_specified (16 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CCL28 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000148672.3. 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	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			15	1		16
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	15	1	0

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CCL28	protein_coding	protein_coding	ENST00000361115	3	35747

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0516	0.709	124958	0	2	124960	0.00000800

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.451	65	76.1	0.855	0.00000414	840
Missense in Polyphen		18	23.886	0.75358		281
Synonymous	0.481	25	28.3	0.885	0.00000181	232
Loss of Function	0.688	2	3.36	0.595	1.41e-7	48

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000545	0.0000545
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.0000545	0.0000545
South Asian	0.0000332	0.0000330
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Chemotactic activity for resting CD4, CD8 T-cells and eosinophils. Binds to CCR3 and CCR10 and induces calcium mobilization in a dose-dependent manner.
• Pathway: Chemokine signaling pathway - Homo sapiens (human);Cytokine-cytokine receptor interaction - Homo sapiens (human);Intestinal immune network for IgA production - Homo sapiens (human);Chemokine signaling pathway;Signaling by GPCR;Signal Transduction;Chemokine receptors bind chemokines;Peptide ligand-binding receptors;Class A/1 (Rhodopsin-like receptors);GPCR ligand binding;G alpha (i) signalling events;GPCR downstream signalling (Consensus)

Recessive Scores

• pRec: 0.102

Intolerance Scores

• loftool: 0.539
• rvis_EVS: 0.26
• rvis_percentile_EVS: 70.06

Haploinsufficiency Scores

• pHI: 0.149
• hipred: N
• hipred_score: 0.112
• ghis: 0.401

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.231

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ccl28

Gene ontology

• Biological process: positive regulation of cell-matrix adhesion;chemotaxis;immune response;G protein-coupled receptor signaling pathway;positive regulation of cytosolic calcium ion concentration;response to nutrient;regulation of signaling receptor activity;cell chemotaxis;negative regulation of leukocyte tethering or rolling
• Cellular component: extracellular region;cell;extracellular exosome
• Molecular function: protein binding;chemokine activity