GPRIN1

G protein regulated inducer of neurite outgrowth 1

Basic information

Region (hg38): 5:176595802-176610156

Links

ENSG00000169258 ∙ NCBI:114787 ∙ OMIM:611239 ∙ HGNC:24835 ∙ Uniprot:Q7Z2K8 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

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		1
missense			92	6		98
nonsense						0
start loss						0
frameshift					2	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)
5-176596854-A-G		not specified	Uncertain significance (Jan 22, 2024)
5-176596856-A-C		not specified	Uncertain significance (Dec 27, 2023)
5-176596858-T-A		not specified	Uncertain significance (Jan 22, 2024)
5-176596915-C-T		not specified	Uncertain significance (Jul 31, 2023)
5-176596939-C-T		not specified	Uncertain significance (Aug 04, 2024)
5-176596983-C-G		not specified	Uncertain significance (Jul 30, 2024)
5-176596984-G-A		not specified	Uncertain significance (Jan 20, 2025)
5-176597118-G-A		not specified	Uncertain significance (Jul 14, 2021)
5-176597125-G-T		not specified	Uncertain significance (Feb 15, 2023)
5-176597136-G-A		not specified	Uncertain significance (Oct 03, 2022)
5-176597148-G-T		not specified	Uncertain significance (May 24, 2024)
5-176597164-C-T		not specified	Uncertain significance (May 02, 2024)
5-176597173-C-T		not specified	Uncertain significance (Jul 05, 2024)
5-176597190-G-A		not specified	Uncertain significance (Jan 26, 2025)
5-176597196-G-A		not specified	Uncertain significance (Jan 07, 2022)
5-176597203-G-T		not specified	Uncertain significance (Aug 06, 2024)
5-176597209-T-C		not specified	Uncertain significance (Oct 03, 2022)
5-176597232-G-T		not specified	Uncertain significance (May 04, 2022)
5-176597240-G-A			Likely benign (May 01, 2022)
5-176597244-C-T		not specified	Uncertain significance (Nov 08, 2022)
5-176597263-C-T		not specified	Likely benign (Dec 04, 2024)
5-176597266-C-T		not specified	Uncertain significance (Dec 27, 2022)
5-176597275-G-A		not specified	Uncertain significance (Mar 11, 2025)
5-176597328-C-T		not specified	Uncertain significance (May 23, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GPRIN1	protein_coding	protein_coding	ENST00000303991	1	14332

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.970	0.0300	68560	8581	48607	125748	0.262

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.338	496	518	0.958	0.0000294	6278
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	1.04	0.750
Ashkenazi Jewish	0.544	0.272
East Asian	0.654	0.328
Finnish	0.410	0.202
European (Non-Finnish)	0.530	0.266
Middle Eastern	0.654	0.328
South Asian	0.541	0.269
Other	0.544	0.268

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

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

Mouse Genome Informatics

• Gene name: Gprin1

Gene ontology

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