GPRIN1

protein-coding

G protein regulated inducer of neurite outgrowth 1

Gene summary

Predicted to enable phosphoprotein binding activity. Predicted to be involved in neuron projection development. Located in plasma membrane. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_052899.3

Inheritance

—

ClinVar variants

U:155B:12

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.1

Max pathogenic AF

—

Genomic locus

chr5:176,595,802-176,610,156

External References & Databases

Ensembl (ENSG00000169258)

Transcript & Mutation Effects

hg38 • Region Span ~14.4 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 GPRIN1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 165

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_052899.3. 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				1 clinvar		1
missense			154 clinvar	11 clinvar		165
nonsense						0
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)						0
Total	0	0	155	12	0	167

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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_052899.3	RefSeq	NP_443131.2	1	MANE Select
ENST00000303991.5	Ensembl	ENSP00000305839.4	1	MANE Select
ENST00000926001.1	Ensembl	ENSP00000596060.1	1	Standard
ENST00000926002.1	Ensembl	ENSP00000596061.1	1	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

MECP2 and Associated Rett Syndrome

Biological Process

neuron projection development

Molecular Function

phosphoprotein binding

Cellular Component

plasma membrane
growth cone

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000303991
Coding exons: 1
Length: 14332
Individuals with no LoFs: 68560
Homozygous LoFs: 8581
Heterozygous LoFs: 48607
Defined: 125748
p: 0.262

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.338	496	518	0.958	0.0000294	6278
Missense (PolyPhen)		85	136.12	0.62444		1968
Synonymous	0.307	228	234	0.974	0.0000157	2313
Loss of Function	3.69	2	19.7	0.102	9.88e-7	326

Population LoF Frequency

Population	CAF	p-value	Status
African	0.59	0.30	notable
Latino/Admixed American	0.45	0.23	notable
Ashkenazi Jewish	0.54	0.27	notable
East Asian	0.65	0.33	notable
Finnish	0.41	0.20	notable
European (Non-Finnish)	0.53	0.27	notable
South Asian	0.54	0.27	notable
Other	0.54	0.27	notable

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May be involved in neurite outgrowth. {ECO:0000250}.;

Recessive Scores

pRec: 0.0800

Intolerance Scores

LoFtool: 0.487
RVIS EVS: 0.16
RVIS percentile EVS: 64.92

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.0646

Gene Damage Prediction

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