HDLBP

high density lipoprotein binding protein

Basic information

Region (hg38): 2:241227263-241317061

Previous symbols: [ "VGL" ]

Links

ENSG00000115677 ∙ NCBI:3069 ∙ OMIM:142695 ∙ HGNC:4857 ∙ Uniprot:Q00341 ∙ 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 HDLBP gene.

• Inborn genetic diseases (26 variants)
• not provided (19 variants)
• HDLBP-related condition (3 variants)
• not specified (1 variants)
• Fine-Lubinsky syndrome (1 variants)
• Marfanoid habitus and intellectual disability (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HDLBP 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				7	4	11
missense			31	2	3	36
nonsense			1			1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)			1			1
splice region					1	1
non coding					1	1
Total	0	0	33	9	8

Variants in HDLBP

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

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

Position	Type	Phenotype	Significance	ClinVar
2-241229678-T-C		not specified	Uncertain significance (Nov 07, 2022)
2-241230153-G-A		HDLBP-related disorder	Likely benign (Mar 14, 2019)
2-241230213-C-T		HDLBP-related disorder	Likely benign (Jun 02, 2023)
2-241230797-G-A		not specified	Uncertain significance (Jan 31, 2024)
2-241230821-C-T		not specified	Uncertain significance (Nov 15, 2021)
2-241230840-G-A		HDLBP-related disorder	Likely benign (May 08, 2019)
2-241233832-G-A		HDLBP-related disorder	Benign (Nov 11, 2019)
2-241233858-C-T		HDLBP-related disorder	Uncertain significance (Oct 02, 2023)
2-241233872-C-T		not specified	Uncertain significance (Oct 25, 2023)
2-241233891-C-T		not specified	Uncertain significance (May 04, 2022)
2-241233953-C-T		HDLBP-related disorder	Uncertain significance (Jul 16, 2023)
2-241235195-C-T		not specified	Uncertain significance (Dec 13, 2022)
2-241235196-G-A		HDLBP-related disorder	Likely benign (Jan 08, 2020)
2-241235541-G-A		HDLBP-related disorder	Likely benign (Mar 20, 2019)
2-241235555-C-A		not specified	Uncertain significance (Feb 02, 2024)
2-241236606-G-A		HDLBP-related disorder	Benign (Feb 19, 2019)
2-241236626-C-T		not specified	Uncertain significance (Mar 05, 2024)
2-241236652-C-T		not specified	Uncertain significance (Dec 27, 2023)
2-241236663-G-C		not specified	Uncertain significance (Sep 29, 2022)
2-241236713-C-G		not specified	Uncertain significance (Feb 05, 2024)
2-241236734-C-T		not specified	Uncertain significance (Jun 29, 2023)
2-241236740-T-G		not specified	Uncertain significance (Jan 11, 2023)
2-241236773-G-C		HDLBP-related disorder	Benign (Oct 31, 2019)
2-241236777-G-A		HDLBP-related disorder	Likely benign (Sep 18, 2019)
2-241238779-C-G		not specified	Uncertain significance (Aug 04, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HDLBP	protein_coding	protein_coding	ENST00000391975	26	89798

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	2.84e-7	125740	0	8	125748	0.0000318

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	4.10	451	771	0.585	0.0000476	8398
Missense in Polyphen		65	222.89	0.29162		2447
Synonymous	-0.491	298	287	1.04	0.0000188	2432
Loss of Function	6.67	4	59.5	0.0672	0.00000302	713

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000289	0.0000289
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000541	0.0000527
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Appears to play a role in cell sterol metabolism. It may function to protect cells from over-accumulation of cholesterol.
• Pathway: HDL clearance;Plasma lipoprotein clearance;Transport of small molecules;C21-steroid hormone biosynthesis and metabolism;Plasma lipoprotein assembly, remodeling, and clearance (Consensus)

Recessive Scores

• pRec: 0.176

Intolerance Scores

• loftool: 0.461
• rvis_EVS: -1.37
• rvis_percentile_EVS: 4.48

Haploinsufficiency Scores

• pHI: 0.834
• hipred: Y
• hipred_score: 0.664
• ghis: 0.580

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.988

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Hdlbp

Gene ontology

• Biological process: lipid transport;cholesterol metabolic process;high-density lipoprotein particle clearance
• Cellular component: nucleus;cytosol;plasma membrane;high-density lipoprotein particle
• Molecular function: RNA binding;protein binding;lipid binding;cadherin binding