GRID2IP

Grid2 interacting protein, the group of PDZ domain containing|Formins

Basic information

Region (hg38): 7:6496777-6551461

Links

ENSG00000215045 ∙ NCBI:392862 ∙ OMIM:610639 ∙ HGNC:18464 ∙ Uniprot:A4D2P6 ∙ 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 GRID2IP gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GRID2IP 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				9		9
missense			106	3	2	111
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)			1			1
splice region						0
non coding						0
Total	0	0	107	12	2

Variants in GRID2IP

This is a list of pathogenic ClinVar variants found in the GRID2IP region.

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

Position	Type	Phenotype	Significance	ClinVar
7-6497785-G-C		not specified	Uncertain significance (Jan 26, 2023)
7-6497805-C-A		not specified	Uncertain significance (Dec 20, 2023)
7-6498077-A-T		not specified	Uncertain significance (Feb 23, 2023)
7-6498086-G-A		not specified	Uncertain significance (May 15, 2023)
7-6498096-C-T		not specified	Uncertain significance (Dec 19, 2022)
7-6498186-C-G		not specified	Uncertain significance (Dec 14, 2022)
7-6498198-G-A		not specified	Uncertain significance (Mar 15, 2024)
7-6501817-G-A			Likely benign (Aug 01, 2022)
7-6502048-T-A		not specified	Uncertain significance (May 31, 2024)
7-6502066-G-C		not specified	Uncertain significance (Feb 23, 2023)
7-6502092-C-T			Likely benign (Jan 11, 2018)
7-6503035-G-T		not specified	Uncertain significance (May 18, 2023)
7-6503110-G-A			Likely benign (Aug 01, 2022)
7-6503559-C-G		not specified	Uncertain significance (Apr 15, 2024)
7-6503566-G-C			Likely benign (Jan 01, 2023)
7-6503594-G-C		not specified	Uncertain significance (May 23, 2023)
7-6503599-A-T		not specified	Uncertain significance (May 11, 2022)
7-6503642-T-C		not specified	Uncertain significance (Feb 27, 2023)
7-6503654-G-C		not specified	Uncertain significance (Mar 19, 2024)
7-6504853-C-G		not specified	Uncertain significance (Jan 16, 2024)
7-6505823-C-A		not specified	Uncertain significance (Mar 07, 2024)
7-6505886-C-T		not specified	Uncertain significance (May 04, 2023)
7-6505904-C-T		not specified	Uncertain significance (Jul 26, 2021)
7-6508028-C-T		not specified	Uncertain significance (Jun 05, 2023)
7-6508065-G-A		not specified	Uncertain significance (May 06, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GRID2IP	protein_coding	protein_coding	ENST00000457091	22	53975

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.124	0.875	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.07	513	586	0.876	0.0000374	7629
Missense in Polyphen		142	180.04	0.78872		2302
Synonymous	-0.880	280	262	1.07	0.0000178	2568
Loss of Function	4.43	10	40.4	0.247	0.00000210	522

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: Postsynaptic scaffolding protein at the parallel fiber- Purkinje cell synapse, where it may serve to link GRID2 with actin cytoskeleton and various signaling molecules. {ECO:0000250}.

Haploinsufficiency Scores

• pHI: 0.171
• hipred: N
• hipred_score: 0.318

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.703

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Grid2ip
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan)

Gene ontology

• Biological process: long-term synaptic depression
• Cellular component: cell junction;postsynaptic membrane