GPRIN2

G protein regulated inducer of neurite outgrowth 2

Basic information

Region (hg38): 10:46541735-46556658

Previous symbols: [ "KIAA0514" ]

Links

ENSG00000204175 ∙ NCBI:9721 ∙ OMIM:611240 ∙ HGNC:23730 ∙ Uniprot:O60269 ∙ 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 GPRIN2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GPRIN2 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						0
missense			18	1		19
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	18	1	0

Variants in GPRIN2

This is a list of pathogenic ClinVar variants found in the GPRIN2 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-46549412-T-C		not specified	Uncertain significance (Mar 20, 2024)
10-46549424-C-T		not specified	Uncertain significance (Mar 22, 2022)
10-46549425-G-A		not specified	Uncertain significance (Jan 31, 2022)
10-46549440-G-A		not specified	Uncertain significance (Jun 11, 2024)
10-46549478-C-T		not specified	Uncertain significance (Jul 06, 2021)
10-46549535-T-C		not specified	Uncertain significance (Jul 14, 2021)
10-46549602-C-T		not specified	Uncertain significance (Mar 29, 2023)
10-46549682-G-A		not specified	Uncertain significance (Jun 22, 2021)
10-46549682-G-T		not specified	Uncertain significance (Mar 01, 2023)
10-46549686-T-C		not specified	Uncertain significance (Apr 30, 2024)
10-46549721-G-A		not specified	Likely benign (May 17, 2023)
10-46549808-G-T		not specified	Uncertain significance (Feb 21, 2024)
10-46549815-A-G		not specified	Uncertain significance (Jul 05, 2023)
10-46549856-G-A		not specified	Uncertain significance (Dec 19, 2022)
10-46550037-G-T		not specified	Uncertain significance (May 17, 2023)
10-46550049-G-A		not specified	Likely benign (Mar 26, 2024)
10-46550082-C-T		not specified	Uncertain significance (Jun 07, 2023)
10-46550084-G-A		not specified	Uncertain significance (Jan 20, 2023)
10-46550166-C-T		not specified	Uncertain significance (Mar 04, 2024)
10-46550232-G-T		not specified	Uncertain significance (May 12, 2024)
10-46550349-T-A		not specified	Uncertain significance (Mar 07, 2023)
10-46550406-C-G		not specified	Uncertain significance (Apr 15, 2024)
10-46550432-C-T		not specified	Uncertain significance (May 11, 2022)
10-46550552-G-A		not specified	Uncertain significance (Dec 02, 2021)
10-46550640-G-A		not specified	Uncertain significance (Dec 14, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GPRIN2	protein_coding	protein_coding	ENST00000374314	1	11557

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000386	0.382	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.562	256	232	1.10	0.0000127	2659
Missense in Polyphen		82	66.044	1.2416		851
Synonymous	-1.05	111	97.8	1.13	0.00000579	908
Loss of Function	0.423	9	10.5	0.859	5.35e-7	108

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved in neurite outgrowth. {ECO:0000269|PubMed:10480904}.

Recessive Scores

• pRec: 0.0918

Intolerance Scores

• rvis_EVS: 1.09
• rvis_percentile_EVS: 91.9

Haploinsufficiency Scores

• pHI: 0.109
• hipred: N
• hipred_score: 0.123
• ghis: 0.476

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• gene_indispensability_pred: N
• gene_indispensability_score: 0.302

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	High	High	High
Primary Immunodeficiency	High	High	High
Cancer	High	High	High

Mouse Genome Informatics

• Gene name: Gprin2

Gene ontology

• Molecular function: protein binding