HIP1R

huntingtin interacting protein 1 related

Basic information

Region (hg38): 12:122834453-122862961

Links

ENSG00000130787 ∙ NCBI:9026 ∙ OMIM:605613 ∙ HGNC:18415 ∙ Uniprot:O75146 ∙ 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 HIP1R gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HIP1R 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	1	2
missense			74	6	1	81
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				2	1	3
non coding						0
Total	0	0	74	7	2

Variants in HIP1R

This is a list of pathogenic ClinVar variants found in the HIP1R region.

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

Position	Type	Phenotype	Significance	ClinVar
12-122835606-G-T		not specified	Uncertain significance (Sep 20, 2023)
12-122848073-G-A		not specified	Uncertain significance (Jan 03, 2024)
12-122848523-T-C		not specified	Uncertain significance (Mar 07, 2024)
12-122848573-G-A		not specified	Uncertain significance (May 28, 2024)
12-122848592-G-A		not specified	Uncertain significance (Nov 13, 2024)
12-122848802-C-T		not specified	Uncertain significance (Dec 21, 2022)
12-122848832-C-T		not specified	Uncertain significance (Sep 30, 2024)
12-122849889-C-A		not specified	Uncertain significance (Dec 16, 2021)
12-122849891-G-A		not specified	Uncertain significance (Nov 24, 2024)
12-122849897-G-C		not specified	Uncertain significance (Dec 05, 2024)
12-122850849-C-T			Likely benign (Jan 01, 2023)
12-122850873-G-T		not specified	Uncertain significance (Mar 01, 2023)
12-122854035-T-C			Benign (Apr 10, 2018)
12-122854049-G-A		not specified	Uncertain significance (Jul 26, 2021)
12-122854069-G-A		not specified	Uncertain significance (May 02, 2024)
12-122854072-G-A		not specified	Uncertain significance (May 24, 2024)
12-122854929-G-A		not specified	Uncertain significance (Nov 25, 2024)
12-122854949-G-A		not specified	Uncertain significance (Nov 07, 2023)
12-122855084-A-G		not specified	Uncertain significance (Aug 02, 2021)
12-122855095-C-G		not specified	Uncertain significance (May 23, 2023)
12-122855105-A-T		not specified	Uncertain significance (Jun 10, 2022)
12-122855110-G-T		not specified	Uncertain significance (Oct 26, 2022)
12-122855126-G-A		not specified	Uncertain significance (Jul 11, 2023)
12-122855331-G-A		not specified	Uncertain significance (Dec 04, 2024)
12-122855401-C-T		not specified	Uncertain significance (Aug 30, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HIP1R	protein_coding	protein_coding	ENST00000253083	32	28508

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.46e-15	0.999	125645	0	101	125746	0.000402

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0290	656	654	1.00	0.0000433	6871
Missense in Polyphen		200	227.55	0.87894		2429
Synonymous	-1.12	315	291	1.08	0.0000204	2112
Loss of Function	3.12	34	60.1	0.565	0.00000293	689

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000609	0.000605
Ashkenazi Jewish	0.00110	0.00109
East Asian	0.000223	0.000217
Finnish	0.000362	0.000323
European (Non-Finnish)	0.000462	0.000457
Middle Eastern	0.000223	0.000217
South Asian	0.000496	0.000392
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Component of clathrin-coated pits and vesicles, that may link the endocytic machinery to the actin cytoskeleton. Binds 3- phosphoinositides (via ENTH domain). May act through the ENTH domain to promote cell survival by stabilizing receptor tyrosine kinases following ligand-induced endocytosis. {ECO:0000269|PubMed:11889126, ECO:0000269|PubMed:14732715}.
• Pathway: Golgi Associated Vesicle Biogenesis;Clathrin derived vesicle budding;trans-Golgi Network Vesicle Budding;Vesicle-mediated transport;Membrane Trafficking;Clathrin-mediated endocytosis (Consensus)

Recessive Scores

• pRec: 0.105

Intolerance Scores

• loftool: 0.803
• rvis_EVS: -1.05
• rvis_percentile_EVS: 7.6

Haploinsufficiency Scores

• pHI: 0.261
• hipred: Y
• hipred_score: 0.637
• ghis: 0.577

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.753

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Hip1r
• Phenotype: skeleton phenotype; hearing/vestibular/ear phenotype; vision/eye phenotype; normal phenotype; growth/size/body region phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan)

Gene ontology

• Biological process: receptor-mediated endocytosis;apoptotic process;activation of cysteine-type endopeptidase activity involved in apoptotic process;actin filament organization;regulation of endocytosis;negative regulation of actin filament polymerization;positive regulation of protein binding;regulation of actin cytoskeleton organization;negative regulation of Arp2/3 complex-mediated actin nucleation;positive regulation of apoptotic process;negative regulation of apoptotic process;positive regulation of epidermal growth factor receptor signaling pathway;positive regulation of receptor-mediated endocytosis;clathrin coat assembly;protein stabilization;digestive system development;regulation of gastric acid secretion;membrane organization;positive regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway;positive regulation of clathrin coat assembly;regulation of clathrin-dependent endocytosis;positive regulation of platelet-derived growth factor receptor-beta signaling pathway
• Cellular component: cytoplasm;mitochondrion;cytosol;postsynaptic density;apical plasma membrane;AP-2 adaptor complex;clathrin-coated vesicle;actin cortical patch;ruffle membrane;dendrite cytoplasm;neuronal cell body;dendritic spine;intracellular membrane-bounded organelle;perinuclear region of cytoplasm;synaptic membrane
• Molecular function: protein binding;phosphatidylinositol-4,5-bisphosphate binding;phosphatidylinositol-3,4,5-trisphosphate binding;SH3 domain binding;clathrin binding;clathrin light chain binding;phosphatidylinositol binding;clathrin adaptor activity;identical protein binding;protein homodimerization activity;phosphatidylinositol-3,4-bisphosphate binding;protein heterodimerization activity;actin filament binding;phosphatidylinositol-3,5-bisphosphate binding