BLTP3A

gene
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Also known as FLJ20302dJ349A12.1

Summary

BLTP3A (bridge-like lipid transfer protein family member 3A, HGNC:21216) is a protein-coding gene on chromosome 6p21.31, encoding Bridge-like lipid transfer protein family member 3A (Q6BDS2). Tube-forming lipid transport protein which probably mediates the transfer of lipids between membranes at organelle contact sites.

Enables histone deacetylase binding activity and identical protein binding activity. Located in late endosome.

Source: NCBI Gene 54887 — RefSeq curated summary.

At a glance

  • GWAS associations: 72
  • Clinical variants (ClinVar): 245 total
  • MANE Select transcript: NM_017754

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:21216
Approved symbolBLTP3A
Namebridge-like lipid transfer protein family member 3A
Location6p21.31
Locus typegene with protein product
StatusApproved
AliasesFLJ20302, dJ349A12.1
Ensembl geneENSG00000065060
Ensembl biotypeprotein_coding
OMIM619570
Entrez54887

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000192788

RefSeq mRNA: 1 — MANE Select: NM_017754 NM_017754

CCDS: CCDS43455

Canonical transcript exons

ENST00000192788 — 21 exons

ExonStartEnd
ENSE000008495553482165334821815
ENSE000008495573482325734823348
ENSE000008495583483421734834406
ENSE000008495593483472134834861
ENSE000008495603483529434835464
ENSE000010325583482191734821955
ENSE000015360643479208334792294
ENSE000019131173487231334877514
ENSE000022042693485561734855703
ENSE000022402883485772434857917
ENSE000022417793483615634836348
ENSE000022443063485623934856409
ENSE000022519663485732934857470
ENSE000022618153486400234864198
ENSE000022673633486746634867616
ENSE000022868673485679034856929
ENSE000022871643487158434871692
ENSE000023022003485812434859571
ENSE000023032383487181934871925
ENSE000023166393487085434871116
ENSE000023230763486722534867379

Expression profiles

Bgee: expression breadth ubiquitous, 255 present calls, max score 94.87.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 13.3174 / max 182.7254, expressed in 1783 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter IDTPM avgSamples expressed
673809.11211719
2039703.91941509
673790.2859132

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
left ventricle myocardiumUBERON:000656694.87gold quality
tibialis anteriorUBERON:000138593.95gold quality
spermCL:000001993.69gold quality
deltoidUBERON:000147693.36gold quality
epithelial cell of pancreasCL:000008391.89gold quality
vastus lateralisUBERON:000137991.35gold quality
quadriceps femorisUBERON:000137791.23gold quality
biceps brachiiUBERON:000150790.27gold quality
cardiac muscle of right atriumUBERON:000337990.11gold quality
parotid glandUBERON:000183189.98gold quality
parietal pleuraUBERON:000240089.81gold quality
myocardiumUBERON:000234989.55gold quality
visceral pleuraUBERON:000240189.14gold quality
heart right ventricleUBERON:000208089.09gold quality
skeletal muscle tissue of biceps brachiiUBERON:000450288.75gold quality
pancreatic ductal cellCL:000207988.39silver quality
skeletal muscle tissueUBERON:000113488.15gold quality
muscle tissueUBERON:000238586.89gold quality
trabecular bone tissueUBERON:000248386.58gold quality
oviduct epitheliumUBERON:000480486.42gold quality
ileal mucosaUBERON:000033186.11gold quality
germinal epithelium of ovaryUBERON:000130486.03gold quality
upper leg skinUBERON:000426286.01gold quality
palpebral conjunctivaUBERON:000181285.85gold quality
eyeUBERON:000097085.31gold quality
secondary oocyteCL:000065584.85gold quality
Brodmann (1909) area 23UBERON:001355484.80gold quality
skeletal muscle organUBERON:001489284.77gold quality
pigmented layer of retinaUBERON:000178283.70gold quality
adult organismUBERON:000702383.66gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 1.

ExperimentMarker?Max mean expression
E-ANND-3yes5.86

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): TP53

miRNA regulators (miRDB)

251 targeting BLTP3A, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-513A-5P100.0069.772465
HSA-MIR-200B-3P100.0073.312693
HSA-MIR-200C-3P100.0073.352685
HSA-MIR-429100.0073.442698
HSA-MIR-4510100.0066.602050
HSA-MIR-6127100.0066.762188
HSA-MIR-6129100.0066.462080
HSA-MIR-6130100.0066.692012
HSA-MIR-6133100.0066.482064
HSA-MIR-30A-5P100.0076.313233
HSA-MIR-30B-5P100.0076.293248
HSA-MIR-30C-5P100.0076.293248
HSA-MIR-30D-5P100.0076.323233
HSA-MIR-30E-5P100.0076.323242
HSA-MIR-9-5P100.0072.282361
HSA-MIR-29A-3P100.0073.111835
HSA-MIR-29B-3P100.0073.181833
HSA-MIR-29C-3P100.0073.151833
HSA-MIR-1252-5P100.0069.802774
HSA-MIR-340-5P100.0072.504437
HSA-MIR-4668-3P100.0068.742635
HSA-MIR-453199.9969.703181
HSA-MIR-428299.9975.366408
HSA-MIR-3667-3P99.9967.171636
HSA-MIR-27A-3P99.9872.132955
HSA-MIR-27B-3P99.9872.132955
HSA-MIR-998599.9872.112939
HSA-MIR-477599.9875.006394
HSA-MIR-806899.9873.852376
HSA-MIR-3692-3P99.9870.272139

Literature-anchored findings (GeneRIF, showing 5)

  • identified five new systemic lupus erythematosus susceptibility loci (P < 5 x 10(-8)): TNIP1 (odds ratio (OR) = 1.27), PRDM1 (OR = 1.20), JAZF1 (OR = 1.20), UHRF1BP1 (OR = 1.17) and IL10 (OR = 1.19). (PMID:19838195)
  • Cross-population confirmation establishes the involvement of UHRF1BP1 locus in SLE and indicates that distinct alleles are contributing to disease susceptibility. (PMID:21326321)
  • Study shows that SESN1 mRNA, UHRF1BP11 mRNA and miRNA-377-3p levels are prognostically relevant in human papillomavirus-negative head and neck squamous cell carcinoma patients. (PMID:28886272)
  • The association of the UHRF1BP1 gene with systemic lupus erythematosus was replicated in a Han Chinese population from mainland China. (PMID:31691269)
  • PP7080 expedites the proliferation and migration of lung adenocarcinoma cells via sponging miR-670-3p and regulating UHRF1BP1. (PMID:33844396)

Cross-species orthologs

5 orthologs

OrganismSymbolGene ID
danio_reriobltp3aENSDARG00000077011
mus_musculusBltp3aENSMUSG00000039512
rattus_norvegicusBltp3aENSRNOG00000000495
drosophila_melanogasterCG34126FBGN0083962
caenorhabditis_elegansWBGENE00008094

Paralogs (1): BLTP3B (ENSG00000111647)

Protein

Protein identifiers

Bridge-like lipid transfer protein family member 3AQ6BDS2 (reviewed: Q6BDS2)

Alternative names: ICBP90-binding protein 1, UHRF1-binding protein 1, Ubiquitin-like containing PHD and RING finger domains 1-binding protein 1

All UniProt accessions (1): Q6BDS2

UniProt curated annotations — full annotation on UniProt →

Function. Tube-forming lipid transport protein which probably mediates the transfer of lipids between membranes at organelle contact sites. May be involved in the retrograde traffic of vesicle clusters in the endocytic pathway to the Golgi complex.

Subunit / interactions. Homodimer (Potential). Interacts with UHRF1.

Subcellular location. Late endosome.

RefSeq proteins (1): NP_060224* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR026728BLTP3A/BFamily

Pfam: PF24917

UniProt features (26 total): modified residue 7, compositionally biased region 5, region of interest 5, sequence variant 5, coiled-coil region 2, chain 1, domain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q6BDS2-F167.370.31

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 (7): 444, 446, 755, 758, 988, 1103, 1106

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 141 (showing top): GSE45365_NK_CELL_VS_BCELL_DN, TGACCTY_ERR1_Q2, MCBRYAN_PUBERTAL_BREAST_4_5WK_DN, MCBRYAN_PUBERTAL_BREAST_3_4WK_UP, MCBRYAN_PUBERTAL_BREAST_5_6WK_UP, PPAR_DR1_Q2, AACTTT_UNKNOWN, MAF_Q6, HOXA4_Q2, SENESE_HDAC3_TARGETS_DN, GOMF_HISTONE_DEACETYLASE_BINDING, GEORGES_TARGETS_OF_MIR192_AND_MIR215, COUP_DR1_Q6, MCBRYAN_PUBERTAL_BREAST_6_7WK_DN, CCTNTMAGA_UNKNOWN

GO Biological Process (0):

GO Molecular Function (3): identical protein binding (GO:0042802), histone deacetylase binding (GO:0042826), protein binding (GO:0005515)

GO Cellular Component (2): late endosome (GO:0005770), endosome (GO:0005768)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
protein binding1
enzyme binding1
binding1
endosome1
endomembrane system1
cytoplasmic vesicle1

Protein interactions and networks

STRING

686 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
BLTP3APHRF1Q9P1Y6657
BLTP3AILRUNQ9H6K1588
BLTP3ASCUBE3Q8IX30511
BLTP3APXKQ7Z7A4502
BLTP3ATNIP1Q15025499
BLTP3AANKS1AQ92625491
BLTP3AJAZF1Q86VZ6490
BLTP3AUHRF1Q96T88481
BLTP3ACOBLL1Q53SF7476
BLTP3ALYPLAL1Q5VWZ2448
BLTP3AGRB14Q14449445
BLTP3AUBAP2Q5T6F2439
BLTP3ATCP11Q8WWU5435
BLTP3ABANK1Q8NDB2431
BLTP3ARGL2O15211426

IntAct

91 interactions, top by confidence:

ABTypeScore
BCL2L2BCL2L11psi-mi:“MI:0914”(association)0.930
HMG20AKDM1Apsi-mi:“MI:0914”(association)0.730
FOXK2DVL2psi-mi:“MI:0914”(association)0.640
DNAJC7PLD2psi-mi:“MI:0914”(association)0.640
KLHL22TMEM223psi-mi:“MI:0914”(association)0.640
RUVBL1POLR3Apsi-mi:“MI:0914”(association)0.640
RAB9ACHMpsi-mi:“MI:0914”(association)0.610
PCNAPOM121Cpsi-mi:“MI:0914”(association)0.550
CREB3L1AP3B1psi-mi:“MI:0914”(association)0.530
FAM131BAURKApsi-mi:“MI:0914”(association)0.530
RAB30UBBpsi-mi:“MI:0914”(association)0.530
STK16FLGpsi-mi:“MI:0914”(association)0.530
EPB41L5SETD1Apsi-mi:“MI:0914”(association)0.530
STK16UNC119Bpsi-mi:“MI:0914”(association)0.530
CREB3MYO9Apsi-mi:“MI:0914”(association)0.530
MAGEA4MAGEA8psi-mi:“MI:0914”(association)0.530
CBY1CFAP410psi-mi:“MI:0914”(association)0.510
DDX21MED19psi-mi:“MI:2364”(proximity)0.480
BLTP3AH1-2psi-mi:“MI:0915”(physical association)0.400
BLTP3AH2BC9psi-mi:“MI:0915”(physical association)0.400
BLTP3AHMGA1psi-mi:“MI:0915”(physical association)0.400
BLTP3APOLEpsi-mi:“MI:0915”(physical association)0.400
Tube1psi-mi:“MI:0914”(association)0.350
RAPGEF2BDP1psi-mi:“MI:0914”(association)0.350
ZNF644ATP9Apsi-mi:“MI:0914”(association)0.350

BioGRID (112): UHRF1BP1 (Affinity Capture-MS), UHRF1BP1 (Affinity Capture-MS), UHRF1BP1 (Affinity Capture-MS), UHRF1BP1 (Affinity Capture-MS), UHRF1BP1 (Affinity Capture-MS), UHRF1BP1 (Affinity Capture-MS), UHRF1BP1 (Affinity Capture-MS), UHRF1BP1 (Affinity Capture-MS), UHRF1BP1 (Affinity Capture-MS), UHRF1BP1 (Affinity Capture-MS), UHRF1BP1 (Affinity Capture-MS), UHRF1BP1 (Affinity Capture-MS), UHRF1BP1 (Affinity Capture-MS), UHRF1BP1 (Affinity Capture-MS), UHRF1BP1 (Affinity Capture-MS)

ESM2 similar proteins: A0A0R4IES7, A0JN62, A0JNW5, A2AAE1, A2AGL3, A2RSJ4, A2RT67, A2RUS2, A2RV80, B0LPN4, B1H2P5, E7F240, E9Q401, O00507, O94967, P30957, P48553, P51593, Q14161, Q2LD37, Q3TLI0, Q3UHE1, Q3UVG3, Q3UX43, Q5F361, Q5M7Q1, Q5RAQ5, Q5ZJK1, Q658Y4, Q68CL5, Q6BDS2, Q6P6Y1, Q6TEP1, Q6VNB8, Q7TMY8, Q7TSG1, Q7Z6Z7, Q8BHY8, Q8CB44, Q8CGF6

Diamond homologs: A0JNW5, A2RSJ4, Q54KX3, Q6BDS2, Q6NRZ1

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 131 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.

GO biological processes:

GO termPartnersFoldFDR
mitophagy924.1×5e-08
autophagosome maturation823.6×5e-07
autophagosome assembly611.3×4e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance199
Likely benign7
Benign3

Top pathogenic / likely-pathogenic (0)

SpliceAI

3032 predictions. Top by Δscore:

VariantEffectΔscore
6:34821648:TTCA:Tacceptor_loss1.0000
6:34821649:TCAG:Tacceptor_loss1.0000
6:34821650:CA:Cacceptor_loss1.0000
6:34821651:A:ACacceptor_loss1.0000
6:34821651:A:AGacceptor_gain1.0000
6:34821652:G:Aacceptor_loss1.0000
6:34821652:G:GGacceptor_gain1.0000
6:34821652:GGTTC:Gacceptor_gain1.0000
6:34823253:TCA:Tacceptor_loss1.0000
6:34823254:CAGTG:Cacceptor_loss1.0000
6:34823255:A:AGacceptor_gain1.0000
6:34823255:A:ATacceptor_loss1.0000
6:34823256:G:GAacceptor_gain1.0000
6:34823256:GT:Gacceptor_gain1.0000
6:34823256:GTGT:Gacceptor_gain1.0000
6:34823344:CAGAG:Cdonor_loss1.0000
6:34823345:AGAG:Adonor_loss1.0000
6:34823346:GAG:Gdonor_gain1.0000
6:34823346:GAGGT:Gdonor_loss1.0000
6:34823349:GTT:Gdonor_loss1.0000
6:34834403:A:Tdonor_gain1.0000
6:34834716:TCCA:Tacceptor_loss1.0000
6:34834719:A:Cacceptor_loss1.0000
6:34834720:G:Aacceptor_loss1.0000
6:34834857:GAAGA:Gdonor_gain1.0000
6:34834860:GA:Gdonor_gain1.0000
6:34834862:G:GGdonor_gain1.0000
6:34835282:T:TAacceptor_gain1.0000
6:34835289:CTCAG:Cacceptor_loss1.0000
6:34835290:TCAG:Tacceptor_loss1.0000

AlphaMissense

9469 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
6:34821771:T:AW55R1.000
6:34821771:T:CW55R1.000
6:34821795:T:CC63R1.000
6:34821797:C:GC63W1.000
6:34821923:T:AW72R1.000
6:34821923:T:CW72R1.000
6:34821925:G:CW72C1.000
6:34821925:G:TW72C1.000
6:34834745:T:AW185R1.000
6:34834745:T:CW185R1.000
6:34834818:T:CL209P1.000
6:34835351:T:AW243R1.000
6:34835351:T:CW243R1.000
6:34792264:T:AI5N0.999
6:34792279:T:CL10P0.999
6:34792288:T:CL13P0.999
6:34821654:T:CF16L0.999
6:34821655:T:CF16S0.999
6:34821656:C:AF16L0.999
6:34821656:C:GF16L0.999
6:34821702:G:AG32R0.999
6:34821702:G:CG32R0.999
6:34821703:G:AG32E0.999
6:34821715:T:CL36P0.999
6:34821724:T:CL39P0.999
6:34821730:T:AL41Q0.999
6:34821730:T:CL41P0.999
6:34821745:T:CL46P0.999
6:34821796:G:AC63Y0.999
6:34821805:C:AA66D0.999

dbSNP variants (sampled 300 via entrez): RS1000009669 (6:34824451 G>A), RS1000035238 (6:34800822 G>T), RS1000051575 (6:34852911 A>G), RS1000066968 (6:34877564 A>G), RS1000158913 (6:34813047 T>C), RS1000216690 (6:34866979 A>G), RS1000248197 (6:34833279 C>T), RS1000269459 (6:34806574 C>T), RS1000270128 (6:34852652 A>G), RS1000282579 (6:34845619 T>C,G), RS1000299837 (6:34866379 C>T), RS1000305418 (6:34874689 A>G), RS1000335998 (6:34827800 T>G), RS1000369050 (6:34820120 T>C), RS1000402193 (6:34797853 T>G)

Disease associations

OMIM: gene MIM:619570 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

72 associations (top):

StudyTraitp-value
GCST001526_12Fasting blood insulin (BMI interaction)4.000000e-08
GCST001795_32Systemic lupus erythematosus1.000000e-12
GCST002069_12Systemic lupus erythematosus and Systemic sclerosis3.000000e-07
GCST003155_52Systemic lupus erythematosus8.000000e-09
GCST003156_31Systemic lupus erythematosus1.000000e-08
GCST003622_56Systemic lupus erythematosus1.000000e-10
GCST004065_54Waist circumference6.000000e-06
GCST004065_58Waist circumference3.000000e-08
GCST004066_34Hip circumference8.000000e-08
GCST004066_5Hip circumference2.000000e-08
GCST004066_86Hip circumference1.000000e-13
GCST004067_168Hip circumference adjusted for BMI9.000000e-10
GCST004067_181Hip circumference adjusted for BMI3.000000e-06
GCST004067_61Hip circumference adjusted for BMI3.000000e-13
GCST004557_193Body mass index2.000000e-10
GCST004557_222Body mass index8.000000e-08
GCST004557_54Body mass index2.000000e-07
GCST004557_92Body mass index2.000000e-10
GCST004558_215Body mass index (joint analysis main effects and physical activity interaction)2.000000e-09
GCST004558_238Body mass index (joint analysis main effects and physical activity interaction)2.000000e-06
GCST004558_65Body mass index (joint analysis main effects and physical activity interaction)5.000000e-10
GCST004558_92Body mass index (joint analysis main effects and physical activity interaction)3.000000e-07
GCST004559_124Body mass index in physically active individuals2.000000e-07
GCST004559_46Body mass index in physically active individuals2.000000e-07
GCST004559_85Body mass index in physically active individuals4.000000e-06
GCST004603_22Platelet count3.000000e-17
GCST004607_140Plateletcrit2.000000e-17
GCST004867_10Systemic lupus erythematosus2.000000e-08
GCST005185_10Fasting blood insulin7.000000e-06
GCST005194_132Coronary artery disease1.000000e-10

EFO canonical traits (13, from GWAS)

EFO IDTrait name
EFO:0004340body mass index
EFO:0008039BMI-adjusted hip circumference
EFO:0008002physical activity measurement
EFO:0004309platelet count
EFO:0007985platelet crit
EFO:0006941grip strength measurement
EFO:0004341body fat distribution
EFO:0007788BMI-adjusted waist-hip ratio
EFO:0009933Thyroid preparation use measurement
EFO:0007789BMI-adjusted waist circumference
EFO:0010100multisite chronic pain
EFO:0005090basophil count
EFO:0009188Red cell distribution width

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
Valproic Acidaffects expression, decreases expression3
Cyclosporineincreases expression3
Acetaminophendecreases expression, increases expression2
Benzo(a)pyreneaffects methylation2
Estradiolaffects cotreatment, decreases expression, increases expression2
Tobacco Smoke Pollutiondecreases expression, increases expression2
7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxidedecreases expression2
aristolochic acid Idecreases expression1
FR900359affects phosphorylation1
dicrotophosincreases expression1
bisphenol Aaffects cotreatment, increases methylation1
salinomycindecreases expression1
arseniteaffects binding, decreases reaction1
benzo(e)pyreneincreases methylation1
aflatoxin B2increases methylation1
S-(1,2-dichlorovinyl)cysteineincreases expression1
perfluorooctane sulfonic acidincreases expression1
perfluoro-n-nonanoic acidincreases expression1
ICG 001increases expression1
NSC668394increases expression1
Temozolomideincreases expression1
Sunitinibincreases expression1
Fulvestrantaffects cotreatment, increases methylation1
Caffeinedecreases phosphorylation1
Calcitriolincreases expression1
Doxorubicindecreases expression1
Methapyrileneincreases methylation1
1-Methyl-4-phenylpyridiniumincreases expression1
Gold Compoundsdecreases expression1
Antirheumatic Agentsdecreases expression1

Cellosaurus cell lines

2 cell lines: 2 cancer cell line

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

CellosaurusNameCategorySex
CVCL_E9W1A549 BLTP3A KO clone C2Cancer cell lineMale
CVCL_E9W2A549 BLTP3A KO clone D9Cancer cell lineMale

Clinical trials (associated diseases)

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