HDLBP

protein-coding

high density lipoprotein binding protein

Gene summary

The protein encoded by this gene binds high density lipoprotein (HDL) and may function to regulate excess cholesterol levels in cells. The encoded protein also binds RNA and can induce heterochromatin formation. [provided by RefSeq, Mar 2016]

Previous symbols:

MANE transcript

NM_005336.6

Inheritance

—

ClinVar variants

U:154B:28

Top phenotype

HDLBP-related disorder

gnomAD constraint

pLI —, LoF o/e 0.07

Max pathogenic AF

—

Genomic locus

chr2:241,227,264-241,317,061

External References & Databases

Ensembl (ENSG00000115677)

Transcript & Mutation Effects

hg38 • Region Span ~89.8 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to HDLBP variants in ClinVar

5 Conditions Cataloged

not specifiedTotal: 125

HDLBP-related disorderTotal: 30

not providedTotal: 26

Marfanoid habitus and intellectual disabilityTotal: 1

Fine-Lubinsky syndromeTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_005336.6. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			5 clinvar	17 clinvar	4 clinvar	26
missense			133 clinvar	4 clinvar	3 clinvar	140
nonsense			3 clinvar			3
start loss						0
frameshift			4 clinvar			4
splice donor/acceptor (+/-2bp)			9 clinvar			9
Total	0	0	154	21	7	182

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 151 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_005336.6	RefSeq	NP_005327.1	26	MANE Select
ENST00000310931.10	Ensembl	ENSP00000312042.4	26	MANE Select
NM_001243900.3	RefSeq	NP_001230829.1	26	Standard
NM_001320965.3	RefSeq	NP_001307894.1	26	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

HDL clearance
Plasma lipoprotein clearance
Transport of small molecules
C21-steroid hormone biosynthesis and metabolism
Plasma lipoprotein assembly, remodeling, and clearance

Biological Process

lipid transport
cholesterol metabolic process
high-density lipoprotein particle clearance

Molecular Function

RNA binding
protein binding
lipid binding
cadherin binding

Cellular Component

nucleus
cytosol
plasma membrane
high-density lipoprotein particle

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000391975
Coding exons: 26
Length: 89798
Individuals with no LoFs: 125740
Homozygous LoFs: 0
Heterozygous LoFs: 8
Defined: 125748
p: 0.0000318

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	4.10	451	771	0.585	0.0000476	8398
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000029	0.000029	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.000054	0.000053	rare
South Asian	0.000033	0.000033	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Appears to play a role in cell sterol metabolism. It may function to protect cells from over-accumulation of cholesterol.;

Recessive Scores

pRec: 0.176

Intolerance Scores

LoFtool: 0.461
RVIS EVS: -1.37
RVIS percentile EVS: 4.48

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.988

Gene Damage Prediction

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