HDLBP

high density lipoprotein binding protein

Basic information

Region (hg38): 2:241227264-241317061

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.

• not_specified (112 variants)
• HDLBP-related_disorder (28 variants)
• not_provided (19 variants)
• Marfanoid_habitus_and_intellectual_disability (1 variants)
• Fine-Lubinsky_syndrome (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. These statistics are base on transcript: NM_000005336.6. 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	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				17	4	21
missense			112	4	3	119
nonsense			1			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1			1
Total	0	0	114	21	7

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