XCL2

X-C motif chemokine ligand 2, the group of Chemokine ligands

Basic information

Region (hg38): 1:168540768-168543997

Previous symbols: [ "SCYC2" ]

Links

ENSG00000143185 ∙ NCBI:6846 ∙ OMIM:604828 ∙ HGNC:10646 ∙ Uniprot:Q9UBD3 ∙ 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 XCL2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the XCL2 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				1		1
missense			9	1		10
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	9	2	0

Variants in XCL2

This is a list of pathogenic ClinVar variants found in the XCL2 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-168540975-T-A		not specified	Uncertain significance (May 26, 2022)
1-168541046-A-G		not specified	Uncertain significance (Jan 30, 2024)
1-168541059-C-T		not specified	Uncertain significance (Dec 18, 2023)
1-168541076-G-C		not specified	Uncertain significance (Feb 14, 2023)
1-168541076-G-T		not specified	Uncertain significance (Nov 02, 2023)
1-168541103-C-A		not specified	Uncertain significance (Sep 20, 2023)
1-168542040-G-T		not specified	Uncertain significance (Apr 26, 2023)
1-168542079-C-A		not specified	Likely benign (Apr 17, 2023)
1-168542091-G-A			Likely benign (Nov 01, 2022)
1-168542093-C-T		not specified	Uncertain significance (Oct 18, 2021)
1-168543916-A-G		not specified	Uncertain significance (May 30, 2024)
1-168543937-C-T		not specified	Uncertain significance (Apr 25, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
XCL2	protein_coding	protein_coding	ENST00000367819	3	3233

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00907	0.600	125575	0	4	125579	0.0000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.321	69	61.9	1.11	0.00000325	711
Missense in Polyphen		15	13.816	1.0857		183
Synonymous	-0.716	29	24.5	1.18	0.00000130	239
Loss of Function	0.279	3	3.57	0.841	2.36e-7	35

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00000887	0.00000881
Middle Eastern	0.00	0.00
South Asian	0.000113	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Chemotactic activity for lymphocytes but not for monocytes or neutrophils. {ECO:0000250}.
• Pathway: Chemokine signaling pathway - Homo sapiens (human);Cytokine-cytokine receptor interaction - Homo sapiens (human);Signaling by GPCR;Signal Transduction;Chemokine receptors bind chemokines;Peptide ligand-binding receptors;Class A/1 (Rhodopsin-like receptors);GPCR ligand binding;G alpha (q) signalling events;GPCR downstream signalling (Consensus)

Recessive Scores

• pRec: 0.0759

Intolerance Scores

• loftool: 0.693
• rvis_EVS: 0.28
• rvis_percentile_EVS: 71.08

Haploinsufficiency Scores

• pHI: 0.255
• hipred: N
• hipred_score: 0.112
• ghis: 0.393

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0820

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Xcl1
• Phenotype: vision/eye phenotype; digestive/alimentary phenotype; immune system phenotype; liver/biliary system phenotype; hematopoietic system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); endocrine/exocrine gland phenotype

Gene ontology

• Biological process: monocyte chemotaxis;inflammatory response;signal transduction;G protein-coupled receptor signaling pathway;blood circulation;regulation of signaling receptor activity;positive regulation of T cell chemotaxis;neutrophil chemotaxis;positive regulation of GTPase activity;lymphocyte chemotaxis;chemokine-mediated signaling pathway;positive regulation of ERK1 and ERK2 cascade;cellular response to interferon-gamma;cellular response to interleukin-1;cellular response to tumor necrosis factor
• Cellular component: extracellular region;extracellular space
• Molecular function: protein binding;chemokine activity;CCR chemokine receptor binding