GPRIN3

GPRIN family member 3

Basic information

Region (hg38): 4:89236383-89307937

Links

ENSG00000185477 ∙ NCBI:285513 ∙ OMIM:611241 ∙ HGNC:27733 ∙ Uniprot:Q6ZVF9 ∙ 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 GPRIN3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GPRIN3 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			71	5	1	77
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	71	5	1

Variants in GPRIN3

This is a list of pathogenic ClinVar variants found in the GPRIN3 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-89247791-C-G		not specified	Uncertain significance (Jun 03, 2024)
4-89247800-G-A		not specified	Uncertain significance (Aug 27, 2024)
4-89247808-C-G		not specified	Uncertain significance (Jan 17, 2024)
4-89247812-C-T		not specified	Uncertain significance (Jul 20, 2021)
4-89247823-G-A		not specified	Uncertain significance (Jul 14, 2024)
4-89247824-G-A		not specified	Uncertain significance (Oct 12, 2021)
4-89247890-A-C		not specified	Uncertain significance (May 08, 2023)
4-89247899-C-T		not specified	Uncertain significance (Jan 24, 2024)
4-89247916-C-T		not specified	Uncertain significance (Mar 06, 2023)
4-89247926-T-C		not specified	Likely benign (Apr 25, 2023)
4-89248004-C-T		not specified	Uncertain significance (Aug 10, 2021)
4-89248007-C-G		not specified	Likely benign (Aug 12, 2022)
4-89248007-C-T		not specified	Uncertain significance (Jun 06, 2023)
4-89248073-G-A		not specified	Uncertain significance (Jan 31, 2023)
4-89248106-C-A		not specified	Uncertain significance (Jul 14, 2023)
4-89248106-C-T		not specified	Uncertain significance (Dec 20, 2022)
4-89248156-G-C		not specified	Uncertain significance (Nov 24, 2024)
4-89248166-C-T		not specified	Uncertain significance (May 08, 2023)
4-89248193-C-T		not specified	Uncertain significance (May 15, 2023)
4-89248229-C-T		not specified	Uncertain significance (Oct 09, 2024)
4-89248237-G-C		not specified	Uncertain significance (Jan 24, 2024)
4-89248241-G-C		not specified	Uncertain significance (Sep 07, 2024)
4-89248273-C-T		not specified	Uncertain significance (Jul 09, 2021)
4-89248423-A-G		not specified	Uncertain significance (Apr 26, 2024)
4-89248453-C-G		not specified	Uncertain significance (Aug 28, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GPRIN3	protein_coding	protein_coding	ENST00000609438	1	71625

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.06e-13	0.0251	125663	1	82	125746	0.000330

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.01	487	428	1.14	0.0000244	5030
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000919	0.000919
Ashkenazi Jewish	0.0000995	0.0000992
East Asian	0.00103	0.00103
Finnish	0.00	0.00
European (Non-Finnish)	0.000203	0.000202
Middle Eastern	0.00103	0.00103
South Asian	0.000784	0.000752
Other	0.000163	0.000163

dbNSFP

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

Haploinsufficiency Scores

• pHI: 0.105
• hipred: N
• hipred_score: 0.180

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.153

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Gprin3