HDLBP

Summary

HDLBP (high density lipoprotein binding protein, HGNC:4857) is a protein-coding gene on chromosome 2q37.3, encoding Vigilin (Q00341). Appears to play a role in cell sterol metabolism.

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.

Source: NCBI Gene 3069 — RefSeq curated summary.

At a glance

• GWAS associations: 13
• Clinical variants (ClinVar): 104 total
• Druggable target: yes
• MANE Select transcript: NM_005336

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:4857
Approved symbol	HDLBP
Name	high density lipoprotein binding protein
Location	2q37.3
Locus type	gene with protein product
Status	Approved
Aliases	HBP
Ensembl gene	ENSG00000115677
Ensembl biotype	protein_coding
OMIM	142695
Entrez	3069

Gene structure

Transcript identifiers

Ensembl transcripts: 117 — 97 protein_coding, 11 retained_intron, 9 protein_coding_CDS_not_defined

ENST00000310931, ENST00000373292, ENST00000391975, ENST00000391976, ENST00000413241, ENST00000417540, ENST00000420451, ENST00000422080, ENST00000422933, ENST00000423693, ENST00000425989, ENST00000426343, ENST00000427007, ENST00000427183, ENST00000427487, ENST00000428482, ENST00000430918, ENST00000441124, ENST00000442714, ENST00000442730, ENST00000444092, ENST00000449504, ENST00000449864, ENST00000452065, ENST00000452931, ENST00000453141, ENST00000458564, ENST00000459788, ENST00000460826, ENST00000462130, ENST00000467435, ENST00000470482, ENST00000470710, ENST00000471294, ENST00000476807, ENST00000477477, ENST00000479169, ENST00000479894, ENST00000483086, ENST00000484412, ENST00000487169, ENST00000488013, ENST00000488923, ENST00000490697, ENST00000494862, ENST00000496569, ENST00000498595, ENST00000875593, ENST00000875594, ENST00000875595, ENST00000875596, ENST00000875597, ENST00000875598, ENST00000875599, ENST00000875600, ENST00000875601, ENST00000875602, ENST00000875603, ENST00000875604, ENST00000875605, ENST00000875606, ENST00000875607, ENST00000875608, ENST00000875609, ENST00000875610, ENST00000875611, ENST00000875612, ENST00000875613, ENST00000875614, ENST00000875615, ENST00000875616, ENST00000875617, ENST00000875618, ENST00000875619, ENST00000875620, ENST00000875621, ENST00000875622, ENST00000875623, ENST00000875624, ENST00000875625, ENST00000918685, ENST00000918686, ENST00000918687, ENST00000918688, ENST00000918689, ENST00000918690, ENST00000918691, ENST00000944578, ENST00000944579, ENST00000944580, ENST00000944581, ENST00000944582, ENST00000944583, ENST00000944584, ENST00000944585, ENST00000944586, ENST00000944587, ENST00000944588, ENST00000944589, ENST00000944590, ENST00000944591, ENST00000944592, ENST00000944593, ENST00000944594, ENST00000944595, ENST00000944596, ENST00000944597, ENST00000944598, ENST00000944599, ENST00000944600, ENST00000944601, ENST00000944602, ENST00000944603, ENST00000944604, ENST00000944605, ENST00000944606, ENST00000944607

RefSeq mRNA: 6 — MANE Select: NM_005336 NM_001243900, NM_001320965, NM_001320966, NM_001320967, NM_005336, NM_203346

CCDS: CCDS2547, CCDS58760

Canonical transcript exons

ENST00000310931 — 28 exons

Exon	Start	End
ENSE00000787283	241255374	241255580
ENSE00000787286	241252957	241253035
ENSE00000787304	241235121	241235255
ENSE00001381224	241268477	241268541
ENSE00001627910	241315570	241315672
ENSE00001636515	241230153	241230269
ENSE00002286413	241262711	241262926
ENSE00002295413	241264448	241264605
ENSE00002296825	241256600	241256806
ENSE00003462339	241238649	241238787
ENSE00003462881	241235490	241235594
ENSE00003463327	241247056	241247142
ENSE00003499960	241253393	241253497
ENSE00003503899	241248003	241248116
ENSE00003514616	241233820	241233963
ENSE00003517263	241246752	241246883
ENSE00003523414	241239602	241239820
ENSE00003533002	241229833	241229961
ENSE00003542713	241256184	241256399
ENSE00003558434	241236615	241236769
ENSE00003607329	241242460	241242678
ENSE00003617079	241239901	241240122
ENSE00003619058	241230759	241230944
ENSE00003631731	241249841	241249980
ENSE00003636808	241266794	241266906
ENSE00003665823	241255051	241255158
ENSE00003691064	241248244	241248348
ENSE00003920351	241227291	241229687

Expression profiles

Bgee: expression breadth ubiquitous, 304 present calls, max score 99.61.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 181.9572 / max 1484.7063, expressed in 1825 samples.

FANTOM5 promoters (16 alternative TSS)

Promoter ID	TPM avg	Samples expressed
34910	69.6264	1794
34914	61.2444	1823
34913	36.3273	1810
34915	5.2173	1644
34909	3.1634	1164
34907	1.6716	948
34901	1.3340	836
34906	0.9328	551
34905	0.8006	511
34900	0.6854	379

Top tissues by expression

304 total, by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
stromal cell of endometrium	CL:0002255	99.61	gold quality
body of pancreas	UBERON:0001150	99.54	gold quality
calcaneal tendon	UBERON:0003701	99.48	gold quality
adenohypophysis	UBERON:0002196	99.30	gold quality
pituitary gland	UBERON:0000007	99.23	gold quality
left testis	UBERON:0004533	99.23	gold quality
colonic epithelium	UBERON:0000397	99.22	gold quality
cervix squamous epithelium	UBERON:0006922	99.20	silver quality
right testis	UBERON:0004534	99.18	gold quality
right lobe of thyroid gland	UBERON:0001119	99.17	gold quality
hindlimb stylopod muscle	UBERON:0004252	99.15	gold quality
body of stomach	UBERON:0001161	99.13	gold quality
minor salivary gland	UBERON:0001830	99.13	gold quality
endocervix	UBERON:0000458	99.12	gold quality
saliva-secreting gland	UBERON:0001044	99.12	gold quality
right lobe of liver	UBERON:0001114	99.12	gold quality
islet of Langerhans	UBERON:0000006	99.11	gold quality
stomach	UBERON:0000945	99.05	gold quality
apex of heart	UBERON:0002098	99.05	gold quality
gall bladder	UBERON:0002110	99.05	gold quality
adrenal tissue	UBERON:0018303	99.05	gold quality
left lobe of thyroid gland	UBERON:0001120	99.04	gold quality
right uterine tube	UBERON:0001302	99.02	gold quality
pancreas	UBERON:0001264	99.01	gold quality
parotid gland	UBERON:0001831	99.01	gold quality
body of uterus	UBERON:0009853	99.01	gold quality
corpus epididymis	UBERON:0004359	99.00	gold quality
right adrenal gland cortex	UBERON:0035827	99.00	gold quality
left adrenal gland cortex	UBERON:0035825	98.99	gold quality
right adrenal gland	UBERON:0001233	98.96	gold quality

Single-cell (SCXA)

Detected in 7 experiment(s), a significant marker in 6.

Experiment	Marker?	Max mean expression
E-CURD-88	yes	92.32
E-CURD-122	yes	49.30
E-HCAD-4	yes	40.85
E-CURD-112	yes	14.63
E-CURD-46	yes	13.68
E-MTAB-6678	no	3.73
E-ANND-3	no	0.00

Regulation

Is transcription factor: yes

Downstream targets (CollecTRI)

1 targets.

Target	Regulation
CSF1R	Repression

Upstream regulators (CollecTRI, top): CTCF, ESR1, ESR2, MYC, SP1, SREBF1, YY1

miRNA regulators (miRDB)

88 targeting HDLBP, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-340-5P	100.00	72.50	4437
HSA-MIR-4500	99.99	72.72	2367
HSA-MIR-4534	99.99	66.58	1907
HSA-MIR-6077	99.99	68.04	2299
HSA-MIR-19A-3P	99.98	75.33	2762
HSA-MIR-19B-3P	99.98	75.44	2754
HSA-LET-7A-5P	99.98	72.29	1790
HSA-LET-7B-5P	99.98	72.31	1790
HSA-LET-7C-5P	99.98	72.29	1790
HSA-LET-7E-5P	99.98	72.29	1790
HSA-LET-7F-5P	99.98	72.56	1784
HSA-LET-7G-5P	99.98	72.37	1784
HSA-LET-7I-5P	99.98	72.37	1788
HSA-MIR-98-5P	99.98	72.33	1787
HSA-MIR-3688-3P	99.97	72.02	2834
HSA-MIR-4725-3P	99.96	69.53	2520
HSA-MIR-6780B-5P	99.96	69.60	2562
HSA-LET-7D-5P	99.96	71.76	1632
HSA-MIR-4458	99.96	71.64	1650
HSA-MIR-6778-3P	99.96	67.29	2693
HSA-MIR-4267	99.96	66.53	2368
HSA-MIR-6721-5P	99.93	68.92	2981
HSA-MIR-3119	99.92	71.34	2390
HSA-MIR-6768-5P	99.92	67.36	1942
HSA-MIR-515-5P	99.92	69.82	2343
HSA-MIR-519E-5P	99.92	69.62	2358
HSA-MIR-4493	99.90	66.48	977
HSA-MIR-9902	99.89	69.15	2250
HSA-MIR-7162-3P	99.89	68.16	1682
HSA-MIR-4271	99.88	68.32	2244

Literature-anchored findings (GeneRIF, showing 17)

• RNA interference studies indicate vigilin is essential for cell viability but is not a global regulator of translation. (PMID:14500828)
• evidence that vigilin is bound to the ribosomal complex. (PMID:15109574)
• C-terminal domain of human vigilin binds to the histone methyltransferase SUV39H1 in vivo;a new model for vigilin-mediated, RNA-induced gene silencing is presented. (PMID:18648073)
• Expression profiles of human VIGILIN, H19, and IGF2 mRNA increased with cell-cycle prograssion. (PMID:19950580)
• identified a competition for binding the 69-nt sequence, through which vigilin and HuR exert opposing effects on c-fms expression, suggesting a role for vigilin in suppression of breast cancer progression (PMID:20974809)
• Vigilin may have a relationship with hepatocellular carcinoma progression and proliferation. (PMID:21500547)
• CTCF may regulate vigilin behavior and thus indirectly influence the binding of HP1alpha to the satellite 2 locus (PMID:24561205)
• progressively upregulated vigilin may serve as a molecular risk marker for hepatocellular carcinoma development, and targeting vigilin may help to inhibit hepatocellular carcinoma cell growth, survival and migration. (PMID:24676454)
• this study shows that vigilin (HDLBP) binds and negatively regulates MICB expression through its 5’UTR, and that vigilin downregulation in target cells leads to NK cell activation against said target cells (PMID:28356383)
• vigilin has been shown to bind over 700 mRNAs and has been associated with cancer progression and cardiovascular disease. (PMID:28975734)
• Our data reveal that vigilin is essential for maintenance of imprinting of IGF2 gene via functional interaction between KH1-7 domains of vigilin and zinc-finger domains of CTCF. (PMID:29157910)
• TSC2 Interacts with HDLBP/Vigilin and Regulates Stress Granule Formation. (PMID:33888601)
• HDLBP binds ER-targeted mRNAs by multivalent interactions to promote protein synthesis of transmembrane and secreted proteins. (PMID:35585045)
• The lipid transporter HDLBP promotes hepatocellular carcinoma metastasis through BRAF-dependent epithelial-mesenchymal transition. (PMID:36122630)
• HDLBP Promotes Hepatocellular Carcinoma Proliferation and Sorafenib Resistance by Suppressing Trim71-dependent RAF1 Degradation. (PMID:36244648)
• HDLBP-stabilized lncFAL inhibits ferroptosis vulnerability by diminishing Trim69-dependent FSP1 degradation in hepatocellular carcinoma. (PMID:36423520)
• Multifaceted functions of RNA-binding protein vigilin in gene silencing, genome stability, and autism-related disorders. (PMID:36758804)

Cross-species orthologs

7 orthologs

Organism	Symbol	Gene ID
danio_rerio	hdlbpa	ENSDARG00000009830
mus_musculus	Hdlbp	ENSMUSG00000034088
rattus_norvegicus	Hdlbp	ENSRNOG00000031479
drosophila_melanogaster	BicC	FBGN0000182
drosophila_melanogaster	Dp1	FBGN0027835
caenorhabditis_elegans		WBGENE00000246
caenorhabditis_elegans		WBGENE00007463

Paralogs (2): BICC1 (ENSG00000122870), ANKS6 (ENSG00000165138)

Protein

Protein identifiers

Vigilin — Q00341 (reviewed: Q00341)

Alternative names: High density lipoprotein-binding protein

All UniProt accessions (24): Q00341, A0A024R4E5, C9J5E5, C9J739, C9JB08, C9JBS3, C9JE93, C9JEJ8, C9JES8, C9JHN6, C9JHS7, C9JHS9, C9JHZ8, C9JIZ1, C9JK79, C9JMQ6, C9JQ82, C9JT62, C9JZI8, H0Y394, H7BZC3, H7C0A4, H7C2D1, H7C3D0

UniProt curated annotations — full annotation on UniProt →

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

Subcellular location. Cytoplasm. Nucleus.

Isoforms (2)

UniProt ID	Names	Canonical?
Q00341-1	1	yes
Q00341-2	2

RefSeq proteins (6): NP_001230829, NP_001307894, NP_001307895, NP_001307896, NP_005327, NP_976221 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR004087	KH_dom	Domain
IPR004088	KH_dom_type_1	Domain
IPR036612	KH_dom_type_1_sf	Homologous_superfamily
IPR057778	KH_Vigilin_N	Domain

Pfam: PF00013, PF24668

UniProt features (96 total): strand 26, helix 21, domain 14, modified residue 13, turn 8, sequence variant 6, region of interest 2, compositionally biased region 2, splice variant 2, initiator methionine 1, chain 1

Structure

Experimental structures (PDB)

8 structures.

PDB	Method	Resolution (Å)
1VIG	SOLUTION NMR
1VIH	SOLUTION NMR
2CTE	SOLUTION NMR
2CTF	SOLUTION NMR
2CTJ	SOLUTION NMR
2CTK	SOLUTION NMR
2CTL	SOLUTION NMR
2CTM	SOLUTION NMR

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q00341-F1	74.80	0.02

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Post-translational modifications (13): 2, 8, 11, 31, 35, 295, 296, 317, 437, 645, 991, 1247, 1252

Function

Pathways and Gene Ontology

Reactome pathways

2 pathways

ID	Pathway
R-HSA-8964011	HDL clearance
R-HSA-9918487	Dengue Virus Genome Translation and Replication

MSigDB gene sets: 236 (showing top): ZHAN_LATE_DIFFERENTIATION_GENES_UP, GRUETZMANN_PANCREATIC_CANCER_DN, MCBRYAN_PUBERTAL_TGFB1_TARGETS_UP, AP2_Q3, RIZKI_TUMOR_INVASIVENESS_3D_DN, MAYBURD_RESPONSE_TO_L663536_UP, MARTINEZ_RB1_TARGETS_UP, MODULE_301, GOBP_LIPID_METABOLIC_PROCESS, FUJII_YBX1_TARGETS_DN, TGGNNNNNNKCCAR_UNKNOWN, MORI_PLASMA_CELL_UP, ACTTTAT_MIR1425P, CTGYNNCTYTAA_UNKNOWN, GOBP_LIPID_LOCALIZATION

GO Biological Process (4): lipid transport (GO:0006869), cholesterol metabolic process (GO:0008203), lipid metabolic process (GO:0006629), steroid metabolic process (GO:0008202)

GO Molecular Function (6): RNA binding (GO:0003723), mRNA binding (GO:0003729), lipid binding (GO:0008289), cadherin binding (GO:0045296), nucleic acid binding (GO:0003676), protein binding (GO:0005515)

GO Cellular Component (4): nucleus (GO:0005634), cytoplasm (GO:0005737), plasma membrane (GO:0005886), high-density lipoprotein particle (GO:0034364)

Reactome top-level categories

Rollup of top-2 pathways:

Category	Pathways
Plasma lipoprotein clearance	1
Dengue Virus Infection	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
binding	3
transport	1
lipid localization	1
sterol metabolic process	1
secondary alcohol metabolic process	1
primary metabolic process	1
lipid metabolic process	1
nucleic acid binding	1
RNA binding	1
cell adhesion molecule binding	1
intracellular membrane-bounded organelle	1
intracellular anatomical structure	1
cellular anatomical structure	1
membrane	1
cell periphery	1
plasma lipoprotein particle	1

Protein interactions and networks

STRING

2735 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
HDLBP	LPL	P06858	835
HDLBP	CETP	P11597	722
HDLBP	APOA2	P02652	721
HDLBP	GPIHBP1	Q8IV16	681
HDLBP	APOA4	P06727	680
HDLBP	APOC3	P02656	677
HDLBP	APOA5	Q6Q788	665
HDLBP	COL6A3	P12111	649
HDLBP	APOA1	P02647	639
HDLBP	APOB	P04114	613
HDLBP	DHX9	Q08211	612
HDLBP	A0A087WVV2	A0A087WVV2	592
HDLBP	COL4A3	Q01955	585
HDLBP	APOC2	P02655	524
HDLBP	APOE	P02649	517

IntAct

233 interactions, top by confidence:

A	B	Type	Score
RFXANK	RFXAP	psi-mi:“MI:0914”(association)	0.780
HSPA8	GAK	psi-mi:“MI:0914”(association)	0.760
CFTR	ESYT2	psi-mi:“MI:2364”(proximity)	0.710
	TOMM70	psi-mi:“MI:0914”(association)	0.690
HRAS	RGL2	psi-mi:“MI:0914”(association)	0.660
RACK1	RIOK3	psi-mi:“MI:0914”(association)	0.640
SNRNP27	UBA6	psi-mi:“MI:0914”(association)	0.530
IL20RA	UPK3BL1	psi-mi:“MI:0914”(association)	0.530
TMEM171	THAP12	psi-mi:“MI:0914”(association)	0.530
WDR59	EPB41L2	psi-mi:“MI:0914”(association)	0.530
USP47	DENR	psi-mi:“MI:0914”(association)	0.530
CYP1A1	SNX3	psi-mi:“MI:0914”(association)	0.530
RPS3	ZNF316	psi-mi:“MI:0914”(association)	0.530
BAG2	HGS	psi-mi:“MI:0914”(association)	0.530
GRK7	HSP90AA1	psi-mi:“MI:0914”(association)	0.530
WASHC3	WASH3P	psi-mi:“MI:0914”(association)	0.530
HDLBP	RAD51	psi-mi:“MI:0915”(physical association)	0.500
DDX21	MED19	psi-mi:“MI:2364”(proximity)	0.480
CSNK2A1	HDLBP	psi-mi:“MI:0217”(phosphorylation reaction)	0.440
MYH16	HDLBP	psi-mi:“MI:0915”(physical association)	0.400
TROVE2	HDLBP	psi-mi:“MI:0915”(physical association)	0.400
HDLBP	GLRB	psi-mi:“MI:0915”(physical association)	0.400
IGSF3	HDLBP	psi-mi:“MI:0915”(physical association)	0.400

BioGRID (973): HDLBP (Affinity Capture-MS), HDLBP (Affinity Capture-MS), HDLBP (Reconstituted Complex), HDLBP (Affinity Capture-MS), HDLBP (Affinity Capture-MS), HDLBP (Affinity Capture-MS), HDLBP (Affinity Capture-MS), HDLBP (Affinity Capture-MS), HDLBP (Affinity Capture-MS), HDLBP (Affinity Capture-MS), HDLBP (Affinity Capture-MS), HDLBP (Two-hybrid), CLUH (Co-fractionation), DDX43 (Co-fractionation), GLMN (Co-fractionation)

ESM2 similar proteins: A3LXL0, A5DM21, C5DIR2, O00425, O42254, O57526, O73932, O74919, O88477, O95758, P04147, P26368, P26369, P42731, P81021, P90727, P90978, P91277, Q00341, Q08CK7, Q54BM2, Q5AI15, Q5R439, Q5R9H4, Q5RB68, Q5SF07, Q5YD48, Q5ZLP8, Q66H20, Q6BI95, Q6CDH3, Q6CSV3, Q6FKG4, Q6ICX4, Q74ZS6, Q756R8, Q8BHD7, Q8CGX0, Q8VDJ3, Q8WN55

Diamond homologs: A0A0B4KGY6, A6ZKR5, B3LNH0, C5DIR2, C7GND0, C8Z3W4, O00425, O19048, O42254, O57526, O73932, O75179, O88477, P38199, P57721, P57722, P57723, P57724, P60335, Q00341, Q0VCU0, Q15365, Q15366, Q5E9A3, Q5R439, Q5ZLP8, Q61990, Q8CGX0, Q8UVD9, Q96AE4, Q99NH0, Q9CPN8, Q9NZI8, Q9PW80, Q9UNW9, P81021, Q8VDJ3, Q9Z1A6, A4SG26, A6VCJ6

SIGNOR signaling

7 interactions.

A	Effect	B	Mechanism
HDLBP	up-regulates	HDL_assembly
HDLBP	“up-regulates activity”	CTCF	binding
HDLBP	up-regulates	Chromatine_condensation
HDLBP	up-regulates	Chromosome_segregation
HDLBP	“down-regulates quantity by repression”	CSF1R	“transcriptional regulation”
HDLBP	“up-regulates activity”	RAD51	binding
HDLBP	“up-regulates activity”	BRCA1	binding

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 223 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

Pathway	Partners	Fold	FDR
Signaling by high-kinase activity BRAF mutants	6	14.0×	1e-03
MAP2K and MAPK activation	6	12.6×	1e-03
Signaling by RAF1 mutants	6	12.3×	1e-03
Signaling by BRAF and RAF1 fusions	9	11.3×	7e-05
Signaling by moderate kinase activity BRAF mutants	6	11.2×	2e-03
Paradoxical activation of RAF signaling by kinase inactive BRAF	6	11.2×	2e-03
Signaling downstream of RAS mutants	6	11.2×	2e-03
mRNA Splicing - Major Pathway	13	5.2×	5e-04

GO biological processes:

GO term	Partners	Fold	FDR
stress granule assembly	6	18.7×	5e-04
negative regulation of extrinsic apoptotic signaling pathway via death domain receptors	5	15.1×	4e-03
activation of innate immune response	5	12.5×	7e-03
negative regulation of translation	12	12.2×	4e-07
positive regulation of interferon-beta production	6	12.2×	3e-03
cytoplasmic translation	8	7.7×	3e-03
mRNA splicing, via spliceosome	12	5.7×	7e-04

Disease & clinical

Clinical variants and AI predictions

ClinVar

104 variants total. Per-class counts are floors (≥ shown; pagination cap):

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	65
Likely benign	18
Benign	8

Top pathogenic / likely-pathogenic (0)

SpliceAI

5246 predictions. Top by Δscore:

Variant	Effect	Δscore
2:241229828:CTGAC:C	donor_loss	1.0000
2:241229832:C:CT	donor_loss	1.0000
2:241229832:CCTT:C	donor_gain	1.0000
2:241229839:A:AC	donor_gain	1.0000
2:241229840:C:CC	donor_gain	1.0000
2:241229840:CTG:C	donor_gain	1.0000
2:241229958:CTAG:C	acceptor_gain	1.0000
2:241229959:TAG:T	acceptor_gain	1.0000
2:241229960:AG:A	acceptor_gain	1.0000
2:241229962:C:CA	acceptor_loss	1.0000
2:241229962:C:CC	acceptor_gain	1.0000
2:241229965:C:CT	acceptor_gain	1.0000
2:241229969:C:CT	acceptor_gain	1.0000
2:241229970:A:T	acceptor_gain	1.0000
2:241230151:A:AC	donor_gain	1.0000
2:241230152:C:CA	donor_gain	1.0000
2:241230152:CGT:C	donor_gain	1.0000
2:241230155:ATT:A	donor_gain	1.0000
2:241230160:T:TA	donor_gain	1.0000
2:241230269:CCT:C	acceptor_loss	1.0000
2:241230271:T:A	acceptor_loss	1.0000
2:241230754:CTCA:C	donor_loss	1.0000
2:241230755:TCACC:T	donor_loss	1.0000
2:241230756:CA:C	donor_loss	1.0000
2:241230940:TGGGG:T	acceptor_gain	1.0000
2:241230941:GGGG:G	acceptor_gain	1.0000
2:241230942:GGG:G	acceptor_gain	1.0000
2:241230943:GG:G	acceptor_gain	1.0000
2:241230945:C:CC	acceptor_gain	1.0000
2:241233816:TCACC:T	donor_loss	1.0000

AlphaMissense

8426 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
2:241229658:A:C	F1250L	1.000
2:241229658:A:T	F1250L	1.000
2:241229659:A:C	F1250C	1.000
2:241229660:A:G	F1250L	1.000
2:241229856:A:G	W1233R	1.000
2:241229856:A:T	W1233R	1.000
2:241230166:A:G	L1193P	1.000
2:241230188:C:G	A1186P	1.000
2:241230211:C:A	G1178V	1.000
2:241230211:C:T	G1178E	1.000
2:241230212:C:A	G1178W	1.000
2:241230212:C:G	G1178R	1.000
2:241230212:C:T	G1178R	1.000
2:241230217:A:T	V1176E	1.000
2:241230223:A:T	V1174D	1.000
2:241230793:C:A	G1147V	1.000
2:241230793:C:T	G1147D	1.000
2:241230802:C:A	G1144V	1.000
2:241230802:C:T	G1144D	1.000
2:241230803:C:G	G1144R	1.000
2:241230805:A:T	I1143N	1.000
2:241230883:A:T	I1117K	1.000
2:241230895:G:T	A1113D	1.000
2:241230896:C:G	A1113P	1.000
2:241230919:C:A	G1105V	1.000
2:241230919:C:T	G1105E	1.000
2:241230920:C:A	G1105W	1.000
2:241230920:C:G	G1105R	1.000
2:241230920:C:T	G1105R	1.000
2:241230925:A:T	I1103N	1.000

dbSNP variants (sampled 300 via entrez): RS1000012733 (2:241260276 G>A), RS1000089054 (2:241293598 C>A,T), RS1000099145 (2:241293999 A>G), RS1000149747 (2:241255242 G>T), RS1000153331 (2:241304388 A>G,T), RS1000173862 (2:241304980 A>G,T), RS1000180117 (2:241308662 C>G), RS1000211122 (2:241308898 A>G), RS1000242513 (2:241259890 T>C), RS1000271105 (2:241281589 A>G), RS1000273750 (2:241233637 T>G), RS1000295812 (2:241287847 A>G), RS1000301626 (2:241275000 A>G), RS1000325053 (2:241269537 A>C), RS1000342343 (2:241271012 G>A)

Disease associations

OMIM: gene MIM:142695 | disease phenotypes: MIM:601353

GenCC curated gene-disease

Mondo (1): Fine-Lubinsky syndrome (MONDO:0011049)

Orphanet (1): Aymé-Gripp syndrome (Orphanet:1272)

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

13 associations (top):

Study	Trait	p-value
GCST001942_6	Prostate cancer	5.000000e-09
GCST003194_5	Fibrinogen levels	8.000000e-19
GCST004121_23	Fibrinogen levels	2.000000e-14
GCST004500_123	Waist circumference adjusted for BMI (adjusted for smoking behaviour)	7.000000e-12
GCST004501_57	Waist circumference adjusted for BMI (joint analysis main effects and smoking interaction)	3.000000e-11
GCST004504_55	Waist circumference adjusted for BMI in non-smokers	9.000000e-11
GCST005580_156	Intraocular pressure	7.000000e-09
GCST010241_31	Apolipoprotein A1 levels	8.000000e-17
GCST010242_313	HDL cholesterol levels	4.000000e-14
GCST010243_122	Apolipoprotein B levels	3.000000e-11
GCST90002396_185	Mean reticulocyte volume	9.000000e-16
GCST90002397_642	Mean spheric corpuscular volume	2.000000e-20
GCST90011900_177	Serum alkaline phosphatase levels	3.000000e-10

EFO canonical traits (8, from GWAS)

EFO ID	Trait name
EFO:0004318	smoking behavior
EFO:0007789	BMI-adjusted waist circumference
EFO:0004695	intraocular pressure measurement
EFO:0004614	apolipoprotein A 1 measurement
EFO:0004612	high density lipoprotein cholesterol measurement
EFO:0004615	apolipoprotein B measurement
EFO:0010701	mean reticulocyte volume
EFO:0004533	alkaline phosphatase measurement

MeSH disease descriptors (1)

Descriptor	Name	Tree numbers
C537933	Fine-Lubinsky syndrome (supp.)

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL4295796 (SINGLE PROTEIN)

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

58 total (human), top 30 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
sodium arsenite	affects reaction, affects expression, affects binding, increases activity, increases abundance (+5 more)	6
Valproic Acid	decreases expression, affects expression, decreases methylation, affects cotreatment	6
bisphenol A	increases expression, decreases methylation	3
mercuric bromide	decreases expression, affects cotreatment	2
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, decreases expression	2
Vorinostat	decreases expression, affects cotreatment	2
Cadmium Chloride	increases abundance, increases expression	2
FR900359	affects phosphorylation	1
bisphenol F	affects cotreatment, decreases expression	1
2,4,6-tribromophenol	decreases expression	1
methylmercuric chloride	decreases expression	1
triphenyl phosphate	affects expression	1
sodium arsenate	decreases expression	1
pyrogallol 1,3-dimethyl ether	affects cotreatment, decreases expression	1
beta-lapachone	decreases expression, increases expression	1
tetrabromobisphenol A	decreases expression	1
perfluorooctanoic acid	decreases expression	1
nivalenol	decreases expression	1
phenethyl isothiocyanate	decreases expression	1
di-n-butylphosphoric acid	affects expression	1
2,3,5-(triglutathion-S-yl)hydroquinone	decreases ADP-ribosylation	1
CGP 52608	increases reaction, affects binding	1
bisphenol B	increases expression	1
dorsomorphin	affects cotreatment, decreases expression	1
pentabrominated diphenyl ether 100	decreases expression	1
hexabrominated diphenyl ether 153	decreases expression	1
bisphenol S	increases methylation	1
LDN 193189	affects cotreatment, decreases expression	1
tianma gouteng yin	increases expression	1
bisphenol AF	increases expression	1

ChEMBL screening assays

2 unique, capped per target: 2 binding

Representative assays (with source publication via chembl_document):

Assay ID	Type	Description	Source paper
CHEMBL4119026	Binding	Binding affinity to HDLBP in human NCI-H358 cells at 1 uM by mass spectrometry based pull down assay	Studies of TAK1-centered polypharmacology with novel covalent TAK1 inhibitors. — Bioorg Med Chem

Cellosaurus cell lines

4 cell lines: 4 cancer cell line

First 10 cell lines (id-ordered, not curated):

Cellosaurus	Name	Category	Sex
CVCL_E1YW	HAP1 HDLBP (-) 1	Cancer cell line	Male
CVCL_E1YX	HAP1 HDLBP (-) 2	Cancer cell line	Male
CVCL_E1YY	HAP1 HDLBP (-) 3	Cancer cell line	Male
CVCL_E1YZ	HAP1 HDLBP (-) 4	Cancer cell line	Male

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.