GRID2IP

protein-coding

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

Gene summary

Glutamate receptor delta-2 (GRID2; MIM 602368) is predominantly expressed at parallel fiber-Purkinje cell postsynapses and plays crucial roles in synaptogenesis and synaptic plasticity. GRID2IP1 interacts with GRID2 and may control GRID2 signaling in Purkinje cells (Matsuda et al., 2006 [PubMed 16835239]).[supplied by OMIM, Mar 2008]

MANE transcript

NM_001145118.2

Inheritance

—

ClinVar variants

U:252B:17

Top phenotype

Primary degenerative dementia of the Alzheimer type, presenile onset

gnomAD constraint

pLI —, LoF o/e 0.25

Max pathogenic AF

—

Genomic locus

chr7:6,496,778-6,551,461

External References & Databases

Ensembl (ENSG00000215045)

Transcript & Mutation Effects

hg38 • Region Span ~54.7 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to GRID2IP variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 250

not providedTotal: 12

Primary degenerative dementia of the Alzheimer type, presenile onsetTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001145118.2. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			3 clinvar	11 clinvar		14
missense			246 clinvar	4 clinvar	2 clinvar	252
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	252	15	2	269

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 9 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001145118.2	RefSeq	NP_001138590.1	22	MANE Select
ENST00000457091.3	Ensembl	ENSP00000397351.2	22	MANE Select
NM_001388403.1	RefSeq	NP_001375332.1	21	Standard
NM_001394781.1	RefSeq	NP_001381710.1	21	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

long-term synaptic depression

Cellular Component

cell junction
postsynaptic membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000457091
Coding exons: 22
Length: 53975
Individuals with no LoFs: 0
Homozygous LoFs: 0
Heterozygous LoFs: 0
Defined: 0
p: 0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.07	513	586	0.876	0.0000374	7629
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0	0.0	absent
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

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}.;

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.703

Gene Damage Prediction

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