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.

• not_specified (135 variants)
• not_provided (2 variants)

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. These statistics are base on transcript: NM_000198281.3. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				1		1
missense			125	10	1	136
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	125	11	1

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