GPRIN3

protein-coding

GPRIN family member 3

Gene summary

Predicted to be involved in neuron projection development. Predicted to act upstream of or within several processes, including excitatory chemical synaptic transmission; neuronal action potential; and vitamin D receptor signaling pathway. Predicted to be active in plasma membrane. [provided by Alliance of Genome Resources, Apr 2025]

MANE transcript

NM_198281.3

Inheritance

—

ClinVar variants

U:126B:12

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 1.01

Max pathogenic AF

—

Genomic locus

chr4:89,236,383-89,307,937

External References & Databases

Ensembl (ENSG00000185477)

Transcript & Mutation Effects

hg38 • Region Span ~71.6 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 GPRIN3 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 136

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_198281.3. 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			126 clinvar	10 clinvar	1 clinvar	137
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	126	11	1	138

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 22 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_198281.3	RefSeq	NP_938022.2	1	MANE Select
ENST00000609438.2	Ensembl	ENSP00000476603.1	1	MANE Select
ENST00000333209.4	Ensembl	ENSP00000328672.3	1	Standard
ENST00000715382.1	Ensembl	ENSP00000520450.1	1	Standard

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000609438
Coding exons: 1
Length: 71625
Individuals with no LoFs: 125663
Homozygous LoFs: 1
Heterozygous LoFs: 82
Defined: 125746
p: 0.000330

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-1.01	487	428	1.14	0.0000244	5030
Missense (PolyPhen)		120	109.86	1.0923		1291
Synonymous	-2.12	209	173	1.20	0.0000107	1641
Loss of Function	-0.0226	19	18.9	1.01	8.89e-7	252

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00086	0.00086	rare
Latino/Admixed American	0.000058	0.000058	rare
Ashkenazi Jewish	0.000099	0.000099	rare
East Asian	0.0010	0.0010	notable
Finnish	0	0.0	absent
European (Non-Finnish)	0.00020	0.00020	rare
South Asian	0.00078	0.00075	rare
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

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

Recessive Scores

pRec: 0.0774

Intolerance Scores

LoFtool: 0.710
RVIS EVS: 2.45
RVIS percentile EVS: 98.58

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Indispensability pred.: N
Indispensability score: 0.153

Gene Damage Prediction

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