GPIHBP1

glycosylphosphatidylinositol anchored high density lipoprotein binding protein 1, the group of LY6/PLAUR domain containing

Basic information

Region (hg38): 8:143213218-143217170

Links

ENSG00000277494

∙ NCBI:338328 ∙ OMIM:612757 ∙ HGNC:24945 ∙ Uniprot:Q8IV16 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

hyperlipoproteinemia, type 1D (Strong), mode of inheritance: AR
hyperlipoproteinemia, type 1D (Moderate), mode of inheritance: AR
hyperlipoproteinemia, type 1D (Strong), mode of inheritance: AR
hyperlipoproteinemia, type 1D (Supportive), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Hyperlipoproteinemia, type ID	AR	Cardiovascular; Gastrointestinal	Individuals have been described with severe chylomicronemia/hypertriglyceridemia, and dietary measures (eg, low fat diet) have been described as beneficial related to sequelae such as pancreatitis and colitis, as well as other cardiovascular manifestations	Cardiovascular; Gastrointestinal	17883852; 19304573; 20026666; 20124439; 21816778; 22239554; 24614124; 24847059

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the GPIHBP1 gene.

Cardiovascular_phenotype (104 variants)
not_provided (74 variants)
Hyperlipoproteinemia,_type_1D (23 variants)
GPIHBP1-related_disorder (8 variants)
not_specified (6 variants)
Hyperlipoproteinemia,_type_I (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GPIHBP1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000178172.6. 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	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous			1 clinvar	48 clinvar		49
missense	7 clinvar	4 clinvar	56 clinvar	15 clinvar	1 clinvar	83
nonsense	2 clinvar	3 clinvar	1 clinvar			6
start loss						0
frameshift	2 clinvar	1 clinvar				3
splice donor/acceptor (+/-2bp)	2 clinvar	1 clinvar				3
Total	13	9	58	63	1

Highest pathogenic variant AF is 0.00000868171

Loading clinvar variants...

GnomAD

Source: gnomAD

dbNSFP

Source: dbNSFP

Function: FUNCTION: Plays a key role in the lipolytic processing of chylomicrons. Required for the transport of lipoprotein lipase LPL into the capillary lumen (By similarity). {ECO:0000250}.;
Disease: DISEASE: Hyperlipoproteinemia 1D (HLPP1D) [MIM:615947]: An autosomal recessive disorder characterized by hyperlipoproteinemia, decreased plasma LPL levels in some patients, high plasma triglyceride levels, and refractory fasting chylomicronemia. {ECO:0000269|PubMed:19304573, ECO:0000269|PubMed:20026666, ECO:0000269|PubMed:21314738, ECO:0000269|PubMed:21816778, ECO:0000269|PubMed:22239554, ECO:0000269|PubMed:23831619, ECO:0000269|PubMed:25387803, ECO:0000269|PubMed:27578123}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
Pathway: Signaling by GPCR;Signal Transduction;Metabolism of fat-soluble vitamins;Chylomicron remodeling;Post-translational modification: synthesis of GPI-anchored proteins;Post-translational protein modification;Metabolism of proteins;Metabolism;Transport of small molecules;Metabolism of vitamins and cofactors;Assembly of active LPL and LIPC lipase complexes;Plasma lipoprotein assembly, remodeling, and clearance;Retinoid metabolism and transport;G alpha (i) signalling events;Plasma lipoprotein remodeling;Visual phototransduction;GPCR downstream signalling (Consensus)

Recessive Scores

pRec: 0.0855

Intolerance Scores

loftool: 0.387
rvis_EVS: 0.28
rvis_percentile_EVS: 71.27

Haploinsufficiency Scores

pHI: 0.0978
hipred: N
hipred_score: 0.146
ghis

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: N
gene_indispensability_score: 0.306

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Gpihbp1
Phenotype: homeostasis/metabolism phenotype;

Gene ontology

Biological process: intracellular protein transport;protein import;protein localization to cell surface;cholesterol homeostasis;transcytosis;protein stabilization;regulation of lipoprotein lipase activity;positive regulation of lipoprotein lipase activity;triglyceride homeostasis;response to heparin;protein transmembrane transport;positive regulation of chylomicron remnant clearance
Cellular component: extracellular region;plasma membrane;external side of plasma membrane;membrane;basolateral plasma membrane;apical plasma membrane;anchored component of membrane;anchored component of external side of plasma membrane;high-density lipoprotein particle
Molecular function: lipid binding;protein transmembrane transporter activity;lipase binding;chylomicron binding;lipoprotein particle binding