GPRIN1

G protein regulated inducer of neurite outgrowth 1

Basic information

Region (hg38): 5:176595802-176610156

Links

ENSG00000169258NCBI:114787OMIM:611239HGNC:24835Uniprot:Q7Z2K8AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the GPRIN1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GPRIN1 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
clinvar
1
missense
92
clinvar
6
clinvar
98
nonsense
0
start loss
0
frameshift
2
clinvar
2
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
0
non coding
0
Total 0 0 92 7 2

Variants in GPRIN1

This is a list of pathogenic ClinVar variants found in the GPRIN1 region.

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

Position Type Phenotype Significance ClinVar
5-176596840-A-C not specified Uncertain significance (Sep 11, 2024)3522272
5-176596854-A-G not specified Uncertain significance (Jan 22, 2024)3102016
5-176596856-A-C not specified Uncertain significance (Dec 27, 2023)3102015
5-176596858-T-A not specified Uncertain significance (Jan 22, 2024)3102014
5-176596915-C-T not specified Uncertain significance (Jul 31, 2023)2614970
5-176596939-C-T not specified Uncertain significance (Aug 04, 2024)3522267
5-176596983-C-G not specified Uncertain significance (Jul 30, 2024)3522262
5-176596984-G-A not specified Uncertain significance (Jan 20, 2025)3855487
5-176597118-G-A not specified Uncertain significance (Jul 14, 2021)2350649
5-176597125-G-T not specified Uncertain significance (Feb 15, 2023)2485016
5-176597136-G-A not specified Uncertain significance (Oct 03, 2022)2315458
5-176597148-G-T not specified Uncertain significance (May 24, 2024)3282507
5-176597164-C-T not specified Uncertain significance (May 02, 2024)3282512
5-176597173-C-T not specified Uncertain significance (Jul 05, 2024)3522269
5-176597190-G-A not specified Uncertain significance (Jan 26, 2025)3855494
5-176597196-G-A not specified Uncertain significance (Jan 07, 2022)2270655
5-176597203-G-T not specified Uncertain significance (Aug 06, 2024)3522270
5-176597209-T-C not specified Uncertain significance (Oct 03, 2022)2228396
5-176597232-G-T not specified Uncertain significance (May 04, 2022)2387967
5-176597240-G-A Likely benign (May 01, 2022)2656094
5-176597244-C-T not specified Uncertain significance (Nov 08, 2022)2324350
5-176597263-C-T not specified Likely benign (Dec 04, 2024)3522264
5-176597266-C-T not specified Uncertain significance (Dec 27, 2022)2405538
5-176597275-G-A not specified Uncertain significance (Mar 11, 2025)3855498
5-176597328-C-T not specified Uncertain significance (May 23, 2023)2522528

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
GPRIN1protein_codingprotein_codingENST00000303991 114332
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.9700.0300685608581486071257480.262
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.3384965180.9580.00002946278
Missense in Polyphen85136.120.624441968
Synonymous0.3072282340.9740.00001572313
Loss of Function3.69219.70.1029.88e-7326

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American1.040.750
Ashkenazi Jewish0.5440.272
East Asian0.6540.328
Finnish0.4100.202
European (Non-Finnish)0.5300.266
Middle Eastern0.6540.328
South Asian0.5410.269
Other0.5440.268

dbNSFP

Source: dbNSFP

Function
FUNCTION: May be involved in neurite outgrowth. {ECO:0000250}.;
Pathway
MECP2 and Associated Rett Syndrome (Consensus)

Recessive Scores

pRec
0.0800

Intolerance Scores

loftool
0.487
rvis_EVS
0.16
rvis_percentile_EVS
64.92

Haploinsufficiency Scores

pHI
0.0971
hipred
Y
hipred_score
0.519
ghis
0.553

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
N
gene_indispensability_score
0.0646

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Gprin1
Phenotype

Gene ontology

Biological process
neuron projection development
Cellular component
plasma membrane;growth cone
Molecular function
phosphoprotein binding