GPR15LG

protein-coding

G protein-coupled receptor 15 ligand

Gene summary

Enables chemokine activity. Involved in several processes, including lymphocyte migration; mast cell degranulation; and negative regulation of cell cycle G1/S phase transition. Located in extracellular region. Is active in obsolete extracellular space. [provided by Alliance of Genome Resources, Jun 2026]

Previous symbols:

C10orf99

MANE transcript

NM_207373.3

Inheritance

—

ClinVar variants

U:2

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.34

Max pathogenic AF

—

Genomic locus

chr10:84,173,801-84,185,294

External References & Databases

Ensembl (ENSG00000188373)

Transcript & Mutation Effects

hg38 • Region Span ~11.5 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 GPR15LG variants in ClinVar

0 Conditions Cataloged

No annotated ClinVar phenotypes.

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_207373.3. 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						0
missense						0
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	2	0	0	2

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 7 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_207373.3	RefSeq	NP_997256.1	3	MANE Select
ENST00000372126.4	Ensembl	ENSP00000361199.3	3	MANE Select
ENST00001099778.1	Ensembl	ENSP00000769584.1	3	Standard
ENST00001124701.1	Ensembl	ENSP00000794506.1	3	Standard

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000372126
Coding exons: 3
Length: 11557
Individuals with no LoFs: 125742
Homozygous LoFs: 0
Heterozygous LoFs: 6
Defined: 125748
p: 0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.491	53	43.9	1.21	0.00000220	506
Missense (PolyPhen)		6	5.9663	1.0057		77
Synonymous	0.720	13	16.7	0.776	7.16e-7	175
Loss of Function	1.05	1	2.93	0.341	1.24e-7	34

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.00014	0.00014	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.0000088	0.0000088	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Chemotactic factor that mediates lymphocytes recruitement to epithelia through binding and activation of the G- protein coupled receptor GPR15 (PubMed:28900043, PubMed:28936214). May be a tumor suppressor; together with SUSD2 has a growth inhibitory effect on colon cancer cells which includes G1 cell cycle arrest (PubMed:25351403). {ECO:0000269|PubMed:25351403, ECO:0000269|PubMed:28900043, ECO:0000269|PubMed:28936214}.;

Intolerance Scores

LoFtool: 0.446
RVIS EVS: 0.1
RVIS percentile EVS: 61.28

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N

Gene Damage Prediction

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