HDLBP

high density lipoprotein binding protein

Basic information

Region (hg38): 2:241227264-241317061

Previous symbols: [ "VGL" ]

Links

ENSG00000115677NCBI:3069OMIM:142695HGNC:4857Uniprot:Q00341AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

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.

EffectPLPVUSLBBSum
synonymous
17
clinvar
4
clinvar
21
missense
112
clinvar
4
clinvar
3
clinvar
119
nonsense
1
clinvar
1
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
1
clinvar
1
Total 0 0 114 21 7
Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
HDLBPprotein_codingprotein_codingENST00000391975 2689798
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
1.002.84e-7125740081257480.0000318
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense4.104517710.5850.00004768398
Missense in Polyphen65222.890.291622447
Synonymous-0.4912982871.040.00001882432
Loss of Function6.67459.50.06720.00000302713

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.00002890.0000289
Ashkenazi Jewish0.000.00
East Asian0.000.00
Finnish0.000.00
European (Non-Finnish)0.00005410.0000527
Middle Eastern0.000.00
South Asian0.00003270.0000327
Other0.000.00

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Hdlbp
Phenotype

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