GRIPAP1

GRIP1 associated protein 1

Basic information

Region (hg38): X:48973720-49002265

Links

ENSG00000068400 ∙ NCBI:56850 ∙ OMIM:300408 ∙ HGNC:18706 ∙ Uniprot:Q4V328 ∙ 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 GRIPAP1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GRIPAP1 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				1	4	5
missense			22	3	1	26
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding					1	1
Total	0	0	22	4	6

Variants in GRIPAP1

This is a list of pathogenic ClinVar variants found in the GRIPAP1 region.

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

Position	Type	Phenotype	Significance	ClinVar
X-48974194-T-C			Benign (Aug 08, 2018)
X-48975236-A-G			Benign (Dec 11, 2018)
X-48975236-A-A			Benign (Feb 09, 2018)
X-48976318-G-C		not specified	Uncertain significance (May 20, 2024)
X-48978339-A-G		not specified	Uncertain significance (Jun 29, 2023)
X-48978386-C-G		not specified	Uncertain significance (Jun 07, 2023)
X-48981451-C-T		not specified	Uncertain significance (May 14, 2024)
X-48981646-C-T		not specified	Uncertain significance (Jun 22, 2024)
X-48981663-C-T			Likely benign (Mar 01, 2023)
X-48981676-G-C		not specified	Uncertain significance (Mar 25, 2022)
X-48981803-C-T		Seizure • not specified	Conflicting classifications of pathogenicity (May 28, 2023)
X-48981820-C-T		not specified	Likely benign (Dec 12, 2023)
X-48981829-T-C		not specified	Uncertain significance (Mar 15, 2024)
X-48982998-C-T		not specified	Uncertain significance (May 20, 2024)
X-48983034-A-G			Uncertain significance (Nov 01, 2019)
X-48983239-G-A		Neurodevelopmental disorder • not specified	Uncertain significance (Jul 12, 2022)
X-48983344-G-A		not specified	Uncertain significance (Jan 09, 2024)
X-48983394-G-A		not specified	Uncertain significance (Dec 16, 2023)
X-48983793-T-G		not specified	Uncertain significance (Oct 14, 2023)
X-48983860-C-T		not specified	Uncertain significance (Mar 14, 2024)
X-48985296-T-C		not specified	Uncertain significance (Apr 22, 2022)
X-48985339-C-G			Likely benign (Apr 16, 2018)
X-48987841-C-T		not specified	Uncertain significance (Dec 14, 2023)
X-48988130-T-C			Likely benign (Feb 01, 2023)
X-48988173-C-T		not specified	Uncertain significance (Jun 21, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GRIPAP1	protein_coding	protein_coding	ENST00000376441	26	28542

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.0000183	125728	1	1	125730	0.00000795

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.62	204	340	0.601	0.0000297	5491
Missense in Polyphen		48	119.59	0.40136		1930
Synonymous	1.61	102	125	0.817	0.00000965	1554
Loss of Function	5.53	2	39.5	0.0506	0.00000283	659

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000760	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000129	0.00000879
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Regulates the endosomal recycling back to the neuronal plasma membrane, possibly by connecting early and late recycling endosomal domains and promoting segregation of recycling endosomes from early endosomal membranes. Involved in the localization of recycling endosomes to dendritic spines, thereby playing a role in the maintenance of dendritic spine morphology. Required for the activity-induced AMPA receptor recycling to dendrite membranes and for long-term potentiation and synaptic plasticity (By similarity). {ECO:0000250|UniProtKB:Q9JHZ4}.

Recessive Scores

• pRec: 0.0836

Intolerance Scores

• loftool: 0.131
• rvis_EVS: -0.29
• rvis_percentile_EVS: 33.34

Haploinsufficiency Scores

• pHI: 0.179
• hipred: Y
• hipred_score: 0.707
• ghis: 0.543

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.539

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Gripap1
• Phenotype: 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); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

• Biological process: biological_process;neurotransmitter receptor transport, endosome to postsynaptic membrane;regulation of neurotransmitter receptor transport, endosome to postsynaptic membrane;regulation of recycling endosome localization within postsynapse;regulation of modification of synaptic structure
• Cellular component: nucleoplasm;cytosol;cell junction;axon;dendrite;intracellular membrane-bounded organelle;recycling endosome membrane;blood microparticle;postsynaptic recycling endosome;glutamatergic synapse;extrinsic component of postsynaptic early endosome membrane
• Molecular function: molecular_function;protein binding