BLTP3B

Summary

BLTP3B (bridge-like lipid transfer protein family member 3B, HGNC:29102) is a protein-coding gene on chromosome 12q23.1, encoding Bridge-like lipid transfer protein family member 3B (A0JNW5). Tube-forming lipid transport protein which mediates the transfer of lipids between membranes at organelle contact sites.

Enables GARP complex binding activity; lipid transfer activity; and protein homodimerization activity. Involved in early endosome to Golgi transport and intermembrane lipid transfer. Located in cytosol and early endosome.

Source: NCBI Gene 23074 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 203 total
• MANE Select transcript: NM_015054

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:29102
Approved symbol	BLTP3B
Name	bridge-like lipid transfer protein family member 3B
Location	12q23.1
Locus type	gene with protein product
Status	Approved
Aliases	KIAA0701, SHIP164
Ensembl gene	ENSG00000111647
Ensembl biotype	protein_coding
OMIM	619811
Entrez	23074

Gene structure

Transcript identifiers

Ensembl transcripts: 12 — 10 protein_coding, 1 nonsense_mediated_decay, 1 retained_intron

ENST00000279907, ENST00000356828, ENST00000545232, ENST00000547428, ENST00000547504, ENST00000548045, ENST00000548712, ENST00000550544, ENST00000551973, ENST00000551980, ENST00000927549, ENST00000949295

RefSeq mRNA: 2 — MANE Select: NM_015054 NM_001006947, NM_015054

CCDS: CCDS31882, CCDS31883

Canonical transcript exons

ENST00000279907 — 21 exons

Exon	Start	End
ENSE00000753853	100047943	100048196
ENSE00000818101	100039596	100039789
ENSE00000818102	100047530	100047638
ENSE00000818103	100050168	100050318
ENSE00000922736	100057571	100057746
ENSE00000937790	100097365	100097505
ENSE00000937791	100095667	100095837
ENSE00000994648	100058029	100059533
ENSE00000994649	100051079	100051221
ENSE00000994651	100072672	100072813
ENSE00000994652	100103913	100103951
ENSE00000994654	100084476	100084658
ENSE00000994656	100083016	100083134
ENSE00000994657	100059850	100060043
ENSE00001100209	100102766	100102857
ENSE00001190486	100098352	100098541
ENSE00001220481	100037072	100037755
ENSE00002390690	100142592	100142874
ENSE00003572391	100086275	100086358
ENSE00003608439	100088915	100089095
ENSE00003651950	100108386	100108548

Expression profiles

Bgee: expression breadth ubiquitous, 281 present calls, max score 95.10.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 23.9317 / max 588.4488, expressed in 1803 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
132885	23.9140	1803
132881	0.0177	5

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
cartilage tissue	UBERON:0002418	95.10	gold quality
endothelial cell	CL:0000115	95.04	gold quality
secondary oocyte	CL:0000655	94.37	gold quality
oocyte	CL:0000023	93.40	gold quality
calcaneal tendon	UBERON:0003701	93.21	gold quality
Brodmann (1909) area 23	UBERON:0013554	92.74	gold quality
tendon	UBERON:0000043	91.53	gold quality
choroid plexus epithelium	UBERON:0003911	91.49	gold quality
tibia	UBERON:0000979	91.47	gold quality
monocyte	CL:0000576	90.25	gold quality
mononuclear cell	CL:0000842	90.17	gold quality
leukocyte	CL:0000738	89.69	gold quality
cortical plate	UBERON:0005343	89.50	gold quality
germinal epithelium of ovary	UBERON:0001304	88.85	gold quality
prefrontal cortex	UBERON:0000451	88.53	gold quality
middle temporal gyrus	UBERON:0002771	88.43	gold quality
primary visual cortex	UBERON:0002436	88.17	gold quality
synovial joint	UBERON:0002217	88.09	gold quality
ganglionic eminence	UBERON:0004023	88.05	gold quality
tendon of biceps brachii	UBERON:0008188	87.80	gold quality
adrenal tissue	UBERON:0018303	87.74	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	87.40	gold quality
substantia nigra pars compacta	UBERON:0001965	87.16	gold quality
corpus callosum	UBERON:0002336	87.16	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	87.13	gold quality
islet of Langerhans	UBERON:0000006	87.13	gold quality
gastrocnemius	UBERON:0001388	87.08	gold quality
superior frontal gyrus	UBERON:0002661	86.94	gold quality
ventricular zone	UBERON:0003053	86.76	gold quality
muscle of leg	UBERON:0001383	86.75	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	4.74

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

20 targeting BLTP3B, 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-4531	99.99	69.70	3181
HSA-MIR-3658	99.96	73.87	4379
HSA-MIR-10523-5P	99.91	69.22	2038
HSA-MIR-6499-3P	99.90	66.38	1212
HSA-MIR-205-5P	99.81	70.05	1557
HSA-MIR-4760-5P	99.80	69.88	1619
HSA-MIR-8061	99.63	69.44	1411
HSA-MIR-6740-3P	99.48	68.49	1392
HSA-MIR-491-3P	98.88	68.86	1224
HSA-MIR-6889-3P	98.84	67.35	1198
HSA-MIR-6529-3P	98.68	66.76	1020
HSA-MIR-2467-3P	98.65	67.18	1969
HSA-MIR-6842-3P	98.07	66.33	1325
HSA-MIR-4708-5P	97.77	67.82	831
HSA-MIR-3652	97.71	65.43	1890
HSA-MIR-4430	97.47	65.61	1813
HSA-MIR-939-5P	97.10	65.80	1579
HSA-MIR-1343-5P	96.48	66.06	1506
HSA-MIR-3622B-5P	94.62	64.58	835
HSA-MIR-12115	94.19	66.37	738

Literature-anchored findings (GeneRIF, showing 3)

• UHRF1BP1L was identified as an Syntaxin6 interacting protein (called SHIP164) which regulates sorting form coated early endosomes (PMID:20163565)
• 3 genes identified by association study and supported by ocular expression and/or replication, UHRF1BP1L, PTPRR, and PPFIA2, are novel candidates for myopic development within the MYP3 locus that should be further studied. (PMID:23422819)
• SHIP164 is a chorein motif lipid transfer protein that controls endosome-Golgi membrane traffic. (PMID:35499567)

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	bltp3b	ENSDARG00000004055
mus_musculus	Bltp3b	ENSMUSG00000019951
rattus_norvegicus	Bltp3b	ENSRNOG00000050317
drosophila_melanogaster	CG34126	FBGN0083962
caenorhabditis_elegans		WBGENE00008094

Paralogs (1): BLTP3A (ENSG00000065060)

Protein

Protein identifiers

Bridge-like lipid transfer protein family member 3B — A0JNW5 (reviewed: A0JNW5)

Alternative names: Syntaxin-6 Habc-interacting protein of 164 kDa, UHRF1-binding protein 1-like

All UniProt accessions (8): A0JNW5, A0A0C4DGH6, F8VRN3, F8VW65, F8VWX2, F8W1I2, F8W665, H0YHT7

UniProt curated annotations — full annotation on UniProt →

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

Subunit / interactions. Monomer. Homodimer (via N-terminus). Associates with the Golgi-associated retrograde protein (GARP) complex. Interacts with GARP complex component VPS52. Interacts (via C-terminal coiled-coil domain) with STX6.

Subcellular location. Cytoplasm. Cytosol. Early endosome.

Isoforms (2)

UniProt ID	Names	Canonical?
A0JNW5-1	1	yes
A0JNW5-2	2

RefSeq proteins (2): NP_001006948, NP_055869* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR026728	BLTP3A/B	Family

Pfam: PF24917

UniProt features (23 total): modified residue 5, region of interest 5, compositionally biased region 3, sequence variant 3, splice variant 2, chain 1, domain 1, mutagenesis site 1, sequence conflict 1, coiled-coil region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-A0JNW5-F1	67.53	0.30

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 (5): 414, 418, 774, 935, 1009

Mutagenesis-validated functional residues (1):

Position	Phenotype
772–773	abolishes interaction with stx6. no effect on early endosome location.

Function

Pathways and Gene Ontology

Reactome pathways

5 pathways

ID	Pathway
R-HSA-9696270	RND2 GTPase cycle
R-HSA-162582	Signal Transduction
R-HSA-194315	Signaling by Rho GTPases
R-HSA-9012999	RHO GTPase cycle
R-HSA-9716542	Signaling by Rho GTPases, Miro GTPases and RHOBTB3

MSigDB gene sets: 154 (showing top): TAATAAT_MIR126, AAGTCCA_MIR422B_MIR422A, GOBP_VESICLE_MEDIATED_TRANSPORT, GOBP_EARLY_ENDOSOME_TO_GOLGI_TRANSPORT, GOBP_MEMBRANE_ORGANIZATION, GOBP_RETROGRADE_TRANSPORT_ENDOSOME_TO_GOLGI, GOBP_LIPID_LOCALIZATION, GOBP_CYTOSOLIC_TRANSPORT, MARSON_BOUND_BY_FOXP3_STIMULATED, LINDGREN_BLADDER_CANCER_CLUSTER_1_DN, KRIGE_RESPONSE_TO_TOSEDOSTAT_24HR_UP, GOMF_LIPID_TRANSPORTER_ACTIVITY, GOMF_PROTEIN_DIMERIZATION_ACTIVITY, GOMF_PROTEIN_HOMODIMERIZATION_ACTIVITY, GOBP_GOLGI_VESICLE_TRANSPORT

GO Biological Process (2): early endosome to Golgi transport (GO:0034498), intermembrane lipid transfer (GO:0120009)

GO Molecular Function (4): protein homodimerization activity (GO:0042803), GARP complex binding (GO:0062069), lipid transfer activity (GO:0120013), protein binding (GO:0005515)

GO Cellular Component (4): early endosome (GO:0005769), cytosol (GO:0005829), cytoplasm (GO:0005737), endosome (GO:0005768)

Reactome top-level categories

Rollup of top-4 pathways:

Category	Pathways
RHO GTPase cycle	1
Signaling by Rho GTPases, Miro GTPases and RHOBTB3	1
Signaling by Rho GTPases	1
Signal Transduction	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	2
retrograde transport, endosome to Golgi	1
Golgi vesicle transport	1
lipid transport	1
membrane organization	1
identical protein binding	1
protein dimerization activity	1
protein-containing complex binding	1
transporter activity	1
lipid carrier activity	1
intermembrane lipid transfer	1
binding	1
endosome	1
cytoplasm	1
intracellular anatomical structure	1
endomembrane system	1
cytoplasmic vesicle	1

Protein interactions and networks

STRING

646 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
BLTP3B	STX6	O43752	795
BLTP3B	GPATCH2L	Q9NWQ4	614
BLTP3B	PRR36	Q9H6K5	506
BLTP3B	ZNF829	Q3KNS6	431
BLTP3B	PTPRH	Q9HD43	431
BLTP3B	DEPDC4	Q8N2C3	429
BLTP3B	VPS13C	Q709C8	423
BLTP3B	CCDC121	Q6ZUS5	392
BLTP3B	ZNF700	Q9H0M5	392
BLTP3B	VPS13A	Q96RL7	390
BLTP3B	OR7G3	Q8NG95	376
BLTP3B	ZBED5	Q49AG3	370
BLTP3B	LINC03040	Q8N319	370
BLTP3B	OR5L1	Q8NGL2	370
BLTP3B	GPATCH2	Q9NW75	354

IntAct

74 interactions, top by confidence:

A	B	Type	Score
DYNLL1	BLTP3B	psi-mi:“MI:0914”(association)	0.730
YWHAG	BLTP3B	psi-mi:“MI:0914”(association)	0.640
YWHAG	BLTP3B	psi-mi:“MI:2364”(proximity)	0.640
DYNLL2	BLTP3B	psi-mi:“MI:0914”(association)	0.640
YWHAB	BLTP3B	psi-mi:“MI:2364”(proximity)	0.610
YWHAB	BLTP3B	psi-mi:“MI:0914”(association)	0.610
YWHAH	BLTP3B	psi-mi:“MI:0914”(association)	0.570
YWHAH	BLTP3B	psi-mi:“MI:2364”(proximity)	0.570
YWHAZ	BLTP3B	psi-mi:“MI:0914”(association)	0.530
FNTB	BLTP3B	psi-mi:“MI:0914”(association)	0.530
FAM174A	BLTP3B	psi-mi:“MI:0914”(association)	0.530
CT55	BLTP3B	psi-mi:“MI:0914”(association)	0.530
RAB8B	BLTP3B	psi-mi:“MI:0914”(association)	0.530
MSRB2	BLTP3B	psi-mi:“MI:0914”(association)	0.530
	BLTP3B	psi-mi:“MI:0915”(physical association)	0.400

BioGRID (105): UHRF1BP1L (Affinity Capture-MS), UHRF1BP1L (Affinity Capture-MS), UHRF1BP1L (Affinity Capture-MS), UHRF1BP1L (Affinity Capture-MS), UHRF1BP1L (Affinity Capture-MS), UHRF1BP1L (Affinity Capture-MS), UHRF1BP1L (Affinity Capture-MS), UHRF1BP1L (Affinity Capture-MS), UHRF1BP1L (Affinity Capture-MS), UHRF1BP1L (Affinity Capture-MS), UHRF1BP1L (Affinity Capture-MS), UHRF1BP1L (Affinity Capture-MS), UHRF1BP1L (Affinity Capture-MS), UHRF1BP1L (Affinity Capture-MS), UHRF1BP1L (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, Q08D51, Q21480, Q7Z7G8, Q80TY5, Q96RL7

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 46 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
Activation of BAD and translocation to mitochondria	7	161.5×	8e-13
Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex	7	142.5×	1e-12
SARS-CoV-1 targets host intracellular signalling and regulatory pathways	7	142.5×	1e-12
Activation of BH3-only proteins	7	105.3×	1e-11
RHO GTPases activate PKNs	7	67.3×	3e-10
Intrinsic Pathway for Apoptosis	7	62.1×	5e-10
FOXO-mediated transcription	5	50.9×	6e-07
SARS-CoV-1-host interactions	7	37.3×	2e-08

GO biological processes:

GO term	Partners	Fold	FDR
protein targeting	5	44.7×	3e-05
intracellular protein localization	7	17.9×	3e-05

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	160
Likely benign	5
Benign	13

Top pathogenic / likely-pathogenic (0)

SpliceAI

3932 predictions. Top by Δscore:

Variant	Effect	Δscore
12:100039636:G:C	donor_gain	1.0000
12:100039790:C:CC	acceptor_gain	1.0000
12:100047525:TATA:T	donor_loss	1.0000
12:100047526:ATACC:A	donor_loss	1.0000
12:100047527:TA:T	donor_loss	1.0000
12:100047528:A:T	donor_loss	1.0000
12:100047529:C:CA	donor_loss	1.0000
12:100047529:CCT:C	donor_gain	1.0000
12:100047635:CATC:C	acceptor_gain	1.0000
12:100047637:TC:T	acceptor_gain	1.0000
12:100047638:CC:C	acceptor_gain	1.0000
12:100047941:A:AC	donor_gain	1.0000
12:100047942:C:CC	donor_gain	1.0000
12:100047975:T:C	donor_gain	1.0000
12:100047978:T:TA	donor_gain	1.0000
12:100047989:A:AC	donor_gain	1.0000
12:100047990:C:CC	donor_gain	1.0000
12:100050161:AACTT:A	donor_loss	1.0000
12:100050162:ACTT:A	donor_loss	1.0000
12:100050163:CTT:C	donor_loss	1.0000
12:100050165:TA:T	donor_loss	1.0000
12:100050166:A:AC	donor_gain	1.0000
12:100050166:AC:A	donor_gain	1.0000
12:100050166:ACC:A	donor_loss	1.0000
12:100050167:C:CC	donor_gain	1.0000
12:100050167:CC:C	donor_gain	1.0000
12:100050167:CCA:C	donor_gain	1.0000
12:100050167:CCAA:C	donor_gain	1.0000
12:100050291:C:CT	acceptor_gain	1.0000
12:100050292:A:T	acceptor_gain	1.0000

AlphaMissense

9757 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
12:100088950:A:G	L329P	1.000
12:100095780:A:G	W243R	1.000
12:100095780:A:T	W243R	1.000
12:100097408:A:G	L209S	1.000
12:100097481:A:G	W185R	1.000
12:100097481:A:T	W185R	1.000
12:100098440:A:G	L147P	1.000
12:100098457:G:C	F141L	1.000
12:100098457:G:T	F141L	1.000
12:100098459:A:G	F141L	1.000
12:100103943:C:A	W72C	1.000
12:100103943:C:G	W72C	1.000
12:100103945:A:G	W72R	1.000
12:100103945:A:T	W72R	1.000
12:100108406:A:G	C63R	1.000
12:100108426:A:G	L56P	1.000
12:100108430:A:G	W55R	1.000
12:100108430:A:T	W55R	1.000
12:100108471:A:G	L41S	1.000
12:100108477:A:G	L39S	1.000
12:100108486:A:G	L36P	1.000
12:100108498:C:T	G32E	1.000
12:100108499:C:G	G32R	1.000
12:100108499:C:T	G32R	1.000
12:100059975:A:G	W540R	0.999
12:100059975:A:T	W540R	0.999
12:100059982:G:C	S537R	0.999
12:100059982:G:T	S537R	0.999
12:100059984:T:G	S537R	0.999
12:100086322:A:G	L353P	0.999

dbSNP variants (sampled 300 via entrez): RS1000045654 (12:100041756 A>G), RS1000069958 (12:100130996 A>G), RS1000077599 (12:100112386 A>C), RS1000092507 (12:100072161 C>A), RS1000097527 (12:100036732 A>G), RS1000132056 (12:100049356 G>A,T), RS1000141568 (12:100118278 G>A), RS1000166553 (12:100086556 G>A), RS1000227429 (12:100065164 T>C), RS1000229940 (12:100105995 A>T), RS1000243816 (12:100111924 T>C), RS1000262639 (12:100070733 C>T), RS1000285911 (12:100082674 C>T), RS1000333293 (12:100131354 T>C,G), RS1000356784 (12:100099582 G>A)

Disease associations

OMIM: gene MIM:619811 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

22 total (human), top 22 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects expression, decreases expression	2
GSK-J4	increases expression	1
FR900359	affects phosphorylation	1
bisphenol A	increases methylation	1
arsenite	affects binding, decreases reaction	1
perfluorooctane sulfonic acid	decreases expression	1
abrine	increases expression	1
Grape Seed Proanthocyanidins	affects cotreatment, increases expression	1
jinfukang	decreases expression	1
Resveratrol	affects cotreatment, increases expression	1
Benzo(a)pyrene	decreases methylation	1
Caffeine	decreases phosphorylation	1
Catechin	affects cotreatment, increases expression	1
Lead	increases expression	1
Plant Extracts	increases expression, affects cotreatment	1
Selenium	affects cotreatment, decreases expression	1
Tobacco Smoke Pollution	increases expression	1
Vitamin E	affects cotreatment, decreases expression	1
Cyclosporine	increases expression	1
Gold Compounds	decreases methylation	1
Tungsten Compounds	increases expression	1
Lactic Acid	decreases expression	1

Clinical trials (associated diseases)

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