XCL2

protein-coding

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

Gene summary

Predicted to enable CCR chemokine receptor binding activity and chemokine activity. Predicted to be involved in several processes, including antimicrobial humoral immune response mediated by antimicrobial peptide; cell chemotaxis; and chemokine-mediated signaling pathway. Predicted to be located in extracellular region. Predicted to be active in obsolete extracellular space. [provided by Alliance of Genome Resources, Jun 2026]

Previous symbols:

SCYC2

MANE transcript

NM_003175.4

Inheritance

—

ClinVar variants

U:16B:2

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.84

Max pathogenic AF

—

Genomic locus

chr1:168,540,768-168,543,997

External References & Databases

Ensembl (ENSG00000143185)

Transcript & Mutation Effects

hg38 • Region Span ~3.2 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to XCL2 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 17

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_003175.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous				1 clinvar		1
missense			16 clinvar	1 clinvar		17
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	16	2	0	18

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 5 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_003175.4	RefSeq	NP_003166.1	3	MANE Select
ENST00000367819.3	Ensembl	ENSP00000356793.2	3	MANE Select
ENST00001101058.1	Ensembl	ENSP00000770864.1	3	Standard
ENST00001101059.1	Ensembl	ENSP00000770865.1	2	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Chemokine signaling pathway - Homo sapiens (human)
Cytokine-cytokine receptor interaction - Homo sapiens (human)
Signaling by GPCR
Signal Transduction
Chemokine receptors bind chemokines

Biological Process

monocyte chemotaxis
inflammatory response
signal transduction
G protein-coupled receptor signaling pathway
blood circulation

Molecular Function

protein binding
chemokine activity
CCR chemokine receptor binding

Cellular Component

extracellular region
extracellular space

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000367819
Coding exons: 3
Length: 3233
Individuals with no LoFs: 125575
Homozygous LoFs: 0
Heterozygous LoFs: 4
Defined: 125579
p: 0.0000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.321	69	61.9	1.11	0.00000325	711
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.0000089	0.0000088	rare
South Asian	0.00011	0.000098	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Chemotactic activity for lymphocytes but not for monocytes or neutrophils. {ECO:0000250}.;

Recessive Scores

pRec: 0.0759

Intolerance Scores

LoFtool: 0.693
RVIS EVS: 0.28
RVIS percentile EVS: 71.08

Essentials

Essential (CRISPR): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.0820

Gene Damage Prediction

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