PRELID3B

Summary

PRELID3B (PRELI domain containing 3B, HGNC:15892) is a protein-coding gene on chromosome 20q13.32, encoding PRELI domain containing protein 3B (Q9Y3B1). It is a common-essential gene (DepMap: required in 98.8% of cancer cell lines).

Predicted to enable phosphatidic acid transfer activity. Predicted to be involved in phospholipid transport. Located in mitochondrion.

Source: NCBI Gene 51012 — RefSeq curated summary.

At a glance

• GWAS associations: 9
• Clinical variants (ClinVar): 26 total
• Cancer dependency (DepMap): dependent in 98.8% of screened cell lines (common-essential)
• MANE Select transcript: NM_016045

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:15892
Approved symbol	PRELID3B
Name	PRELI domain containing 3B
Location	20q13.32
Locus type	gene with protein product
Status	Approved
Aliases	dJ543J19.5
Ensembl gene	ENSG00000101166
Ensembl biotype	protein_coding
OMIM	620754
Entrez	51012

Gene structure

Transcript identifiers

Ensembl transcripts: 6 — 4 protein_coding, 1 nonsense_mediated_decay, 1 retained_intron

ENST00000355937, ENST00000371033, ENST00000463057, ENST00000466051, ENST00000852164, ENST00000918587

RefSeq mRNA: 2 — MANE Select: NM_016045 NM_001256403, NM_016045

CCDS: CCDS42893, CCDS58783

Canonical transcript exons

ENST00000355937 — 6 exons

Exon	Start	End
ENSE00000663017	59037191	59037280
ENSE00000845869	59038466	59038634
ENSE00001454162	59033145	59035126
ENSE00001952977	59042699	59042786
ENSE00003459594	59036690	59036760
ENSE00003573436	59036471	59036573

Expression profiles

Bgee: expression breadth ubiquitous, 283 present calls, max score 97.42.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 44.2140 / max 310.2371, expressed in 1815 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
188208	39.5839	1813
188207	4.6301	1281

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
rectum	UBERON:0001052	97.42	gold quality
jejunal mucosa	UBERON:0000399	97.09	gold quality
islet of Langerhans	UBERON:0000006	97.05	gold quality
mucosa of transverse colon	UBERON:0004991	96.46	gold quality
adrenal tissue	UBERON:0018303	95.77	gold quality
lower esophagus mucosa	UBERON:0035834	94.91	gold quality
transverse colon	UBERON:0001157	94.43	gold quality
duodenum	UBERON:0002114	94.41	gold quality
esophagus mucosa	UBERON:0002469	94.17	gold quality
ventricular zone	UBERON:0003053	94.05	gold quality
colonic mucosa	UBERON:0000317	93.89	gold quality
ganglionic eminence	UBERON:0004023	93.74	gold quality
small intestine Peyer’s patch	UBERON:0003454	93.54	gold quality
adenohypophysis	UBERON:0002196	93.44	gold quality
mucosa of sigmoid colon	UBERON:0004993	93.44	gold quality
calcaneal tendon	UBERON:0003701	93.31	gold quality
small intestine	UBERON:0002108	93.29	gold quality
epithelium of nasopharynx	UBERON:0001951	93.28	gold quality
vermiform appendix	UBERON:0001154	93.02	gold quality
monocyte	CL:0000576	92.99	gold quality
mononuclear cell	CL:0000842	92.90	gold quality
intestine	UBERON:0000160	92.83	gold quality
leukocyte	CL:0000738	92.79	gold quality
pituitary gland	UBERON:0000007	92.60	gold quality
large intestine	UBERON:0000059	92.59	gold quality
colon	UBERON:0001155	92.48	gold quality
gall bladder	UBERON:0002110	92.43	gold quality
pancreas	UBERON:0001264	92.39	gold quality
endometrium	UBERON:0001295	92.30	gold quality
left adrenal gland	UBERON:0001234	92.15	gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 2.

Experiment	Marker?	Max mean expression
E-GEOD-111727	yes	459.93
E-ANND-3	no	0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

92 targeting PRELID3B, 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-3613-3P	100.00	76.36	7965
HSA-LET-7A-3P	100.00	74.03	3932
HSA-LET-7B-3P	100.00	74.08	3913
HSA-LET-7F-1-3P	100.00	74.02	3928
HSA-MIR-98-3P	100.00	74.08	3907
HSA-MIR-1277-5P	100.00	73.95	5056
HSA-MIR-3646	100.00	73.56	5283
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-4282	99.99	75.36	6408
HSA-MIR-196A-1-3P	99.99	72.15	2772
HSA-MIR-548P	99.98	72.25	3784
HSA-MIR-4803	99.98	71.99	3117
HSA-MIR-520D-5P	99.98	73.34	4883
HSA-MIR-524-5P	99.98	73.43	4882
HSA-MIR-4775	99.98	75.00	6394
HSA-MIR-607	99.97	73.62	5593
HSA-MIR-548AN	99.97	70.91	2817
HSA-MIR-5688	99.96	73.23	4504
HSA-MIR-495-3P	99.96	72.81	4197
HSA-MIR-548AJ-3P	99.96	73.38	5345
HSA-MIR-548X-3P	99.96	73.38	5345
HSA-MIR-493-5P	99.96	72.47	2382
HSA-MIR-551B-5P	99.96	71.28	3493
HSA-MIR-548J-3P	99.94	72.61	4881
HSA-MIR-141-3P	99.94	72.79	2421
HSA-MIR-200A-3P	99.94	72.68	2420
HSA-MIR-101-3P	99.94	75.03	2230
HSA-MIR-548AE-3P	99.93	72.66	4867
HSA-MIR-548AH-3P	99.93	72.54	4872
HSA-MIR-548AM-3P	99.93	72.54	4872

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 98.8% of screened cell lines, common-essential.

Literature-anchored findings (GeneRIF, showing 2)

• Structural determinants of lipid specificity within Ups/PRELI lipid transfer proteins has been reported. (PMID:30850607)
• SLMO2 is a potential prognostic and immunological biomarker in human pan-cancer. (PMID:38212657)

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	prelid3b	ENSDARG00000009505
mus_musculus	Prelid3b	ENSMUSG00000016257
rattus_norvegicus	Prelid3b	ENSRNOG00000046644
drosophila_melanogaster	slmo	FBGN0029161
caenorhabditis_elegans	F15D3.6	WBGENE00008856

Paralogs (3): PRELID3A (ENSG00000141391), PRELID1 (ENSG00000169230), PRELID2 (ENSG00000186314)

Protein

Protein identifiers

PRELI domain containing protein 3B — Q9Y3B1 (reviewed: Q9Y3B1)

Alternative names: Protein slowmo homolog 2

All UniProt accessions (2): Q9Y3B1, E9PL81

UniProt curated annotations — full annotation on UniProt →

Similarity. Belongs to the slowmo family.

Isoforms (2)

UniProt ID	Names	Canonical?
Q9Y3B1-1	1	yes
Q9Y3B1-2	2

RefSeq proteins (2): NP_001243332, NP_057129* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR006797	PRELI/MSF1_dom	Domain
IPR037365	Slowmo/Ups	Family

Pfam: PF04707

UniProt features (18 total): strand 8, helix 3, turn 2, modified residue 2, chain 1, domain 1, splice variant 1

Structure

Experimental structures (PDB)

1 structures.

PDB	Method	Resolution (Å)
6I4Y	X-RAY DIFFRACTION	2.91

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9Y3B1-F1	82.66	0.38

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 (2): 46, 51

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 152 (showing top): IVANOVA_HEMATOPOIESIS_LATE_PROGENITOR, GOBP_ORGANOPHOSPHATE_ESTER_TRANSPORT, GOCC_MITOCHONDRIAL_ENVELOPE, GOBP_PHOSPHOLIPID_TRANSPORT, GOBP_MEMBRANE_ORGANIZATION, ZHANG_BREAST_CANCER_PROGENITORS_UP, ZHOU_TNF_SIGNALING_4HR, BURTON_ADIPOGENESIS_5, ROSTY_CERVICAL_CANCER_PROLIFERATION_CLUSTER, GOBP_LIPID_LOCALIZATION, BIDUS_METASTASIS_UP, NUYTTEN_EZH2_TARGETS_DN, GOCC_ORGANELLE_ENVELOPE_LUMEN, GOMF_LIPID_TRANSPORTER_ACTIVITY, GOMF_PHOSPHOLIPID_TRANSPORTER_ACTIVITY

GO Biological Process (2): phospholipid transport (GO:0015914), intermembrane lipid transfer (GO:0120009)

GO Molecular Function (2): phosphatidic acid transfer activity (GO:1990050), protein binding (GO:0005515)

GO Cellular Component (2): mitochondrion (GO:0005739), mitochondrial intermembrane space (GO:0005758)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
lipid transport	2
organophosphate ester transport	1
membrane organization	1
phospholipid transfer activity	1
binding	1
cytoplasm	1
intracellular membrane-bounded organelle	1
mitochondrial envelope	1
organelle envelope lumen	1

Protein interactions and networks

STRING

680 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
PRELID3B	TRIAP1	O43715	913
PRELID3B	ATP5F1E	P56381	637
PRELID3B	ZNF575	Q86XF7	574
PRELID3B	ZNF831	Q5JPB2	543
PRELID3B	TRAM2	Q15035	531
PRELID3B	ACAD10	Q6JQN1	526
PRELID3B	STARD7	Q9NQZ5	480
PRELID3B	EDN3	P14138	478
PRELID3B	SLC16A14	Q7RTX9	451
PRELID3B	TMEM14A	Q9Y6G1	449
PRELID3B	TUBB1	Q9H4B7	449
PRELID3B	BLOC1S6	Q9UL45	445
PRELID3B	CMBL	Q96DG6	443
PRELID3B	JOSD1	Q15040	424
PRELID3B	KCNIP3	Q9Y2W7	424

IntAct

7 interactions, top by confidence:

A	B	Type	Score
PRELID3B	TRIAP1	psi-mi:“MI:0914”(association)	0.710
TRIAP1	PRELID3B	psi-mi:“MI:0915”(physical association)	0.710
TRIAP1	JCHAIN	psi-mi:“MI:0914”(association)	0.530

BioGRID (14): TRIAP1 (Affinity Capture-MS), SLMO2 (Affinity Capture-MS), ECH1 (Affinity Capture-MS), SPHKAP (Affinity Capture-MS), C1QBP (Affinity Capture-MS), SLMO2 (Affinity Capture-MS), TRIAP1 (Co-crystal Structure), SLMO2 (Affinity Capture-RNA), SLMO2 (Affinity Capture-MS), SLMO2 (Negative Genetic), SLMO2 (Negative Genetic), SLMO2 (Negative Genetic), SLMO2 (Co-fractionation), SLMO2 (Affinity Capture-RNA)

ESM2 similar proteins: A1A4M6, A5GFX0, A5PJU6, O46689, O88736, P49675, P51557, P53808, P59095, P59096, P70114, P79245, P97826, Q28918, Q28996, Q3U1V6, Q4R5S9, Q58DB0, Q5BKH5, Q5IH13, Q5IH14, Q5R8P9, Q64421, Q6GM21, Q6IQS6, Q6NTS7, Q6P9U4, Q6TMK8, Q8R1R3, Q8VE85, Q8WYK0, Q90673, Q90ZB9, Q94E75, Q96DR4, Q96N28, Q99JV5, Q99NB7, Q9CYY7, Q9DBK0

Diamond homologs: A5GFX0, O59707, P35200, Q4R5S9, Q54G07, Q58DB0, Q6GM21, Q6P9U4, Q6TMK8, Q8VE85, Q96N28, Q9CYY7, Q9V3U9, Q9Y3B1, Q04006, Q0V9N0, Q5BKH5, Q90673, Q9UT07, Q05776, Q32KN9, Q8R107, Q9V579, Q9Y255, Q7PWB1

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	24
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

817 predictions. Top by Δscore:

Variant	Effect	Δscore
20:59035125:CC:C	acceptor_gain	1.0000
20:59035126:CC:C	acceptor_gain	1.0000
20:59035127:C:CA	acceptor_loss	1.0000
20:59035127:C:CC	acceptor_gain	1.0000
20:59035127:C:T	acceptor_gain	1.0000
20:59035128:T:C	acceptor_gain	1.0000
20:59035128:T:TC	acceptor_gain	1.0000
20:59036468:TA:T	donor_loss	1.0000
20:59036469:A:AC	donor_gain	1.0000
20:59036469:ACTT:A	donor_loss	1.0000
20:59036470:C:CC	donor_gain	1.0000
20:59036470:CTTTA:C	donor_gain	1.0000
20:59036569:CAGTT:C	acceptor_gain	1.0000
20:59036570:AGTT:A	acceptor_gain	1.0000
20:59036571:GTT:G	acceptor_gain	1.0000
20:59036572:TT:T	acceptor_gain	1.0000
20:59036572:TTC:T	acceptor_loss	1.0000
20:59036574:C:A	acceptor_loss	1.0000
20:59036574:C:CC	acceptor_gain	1.0000
20:59036575:T:A	acceptor_loss	1.0000
20:59036580:C:CT	acceptor_gain	1.0000
20:59036581:A:T	acceptor_gain	1.0000
20:59036684:A:AC	donor_gain	1.0000
20:59036685:C:CC	donor_gain	1.0000
20:59036685:CTCA:C	donor_gain	1.0000
20:59036687:CA:C	donor_loss	1.0000
20:59036688:A:AC	donor_gain	1.0000
20:59036688:ACTTT:A	donor_loss	1.0000
20:59036689:C:A	donor_loss	1.0000
20:59036689:C:CT	donor_gain	1.0000

AlphaMissense

1272 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
20:59035126:C:G	G156R	0.999
20:59036554:C:G	A128P	0.999
20:59036723:A:G	L110P	0.999
20:59037204:A:G	L93P	0.999
20:59037231:A:T	V84D	0.999
20:59037238:A:G	S82P	0.999
20:59038508:T:A	R53S	0.999
20:59038508:T:G	R53S	0.999
20:59038509:C:G	R53T	0.999
20:59038514:G:C	S51R	0.999
20:59038514:G:T	S51R	0.999
20:59038516:T:G	S51R	0.999
20:59038593:T:C	Y25C	0.999
20:59038594:A:G	Y25H	0.999
20:59038595:T:A	K24N	0.999
20:59038595:T:G	K24N	0.999
20:59038596:T:A	K24I	0.999
20:59038608:G:T	A20D	0.999
20:59038617:A:T	V17D	0.999
20:59038625:C:A	W14C	0.999
20:59038625:C:G	W14C	0.999
20:59038627:A:G	W14R	0.999
20:59038627:A:T	W14R	0.999
20:59035126:C:A	G156C	0.998
20:59036547:A:T	I130N	0.998
20:59036565:A:G	L124S	0.998
20:59036718:A:C	Y112D	0.998
20:59036729:T:A	E108V	0.998
20:59036729:T:G	E108A	0.998
20:59037191:A:C	N97K	0.998

dbSNP variants (sampled 300 via entrez): RS1000268181 (20:59042989 CA>C), RS1000503107 (20:59042984 G>C,T), RS1001054057 (20:59035896 G>A), RS1001106539 (20:59036242 C>T), RS1001621578 (20:59039871 G>A), RS1001953849 (20:59032979 C>A,G), RS1002228053 (20:59044693 A>C,G), RS1002321605 (20:59038422 T>A,C,G), RS1002351232 (20:59038097 A>G), RS1002580379 (20:59044324 A>G), RS1002987931 (20:59041748 A>T), RS1003292184 (20:59041557 A>G), RS1003357617 (20:59039742 T>A), RS1003408282 (20:59041152 A>T), RS1003423601 (20:59032726 C>T)

Disease associations

OMIM: gene MIM:620754 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

9 associations (top):

Study	Trait	p-value
GCST004599_218	Mean platelet volume	2.000000e-10
GCST004616_163	Platelet distribution width	2.000000e-47
GCST004616_164	Platelet distribution width	3.000000e-49
GCST007094_231	Diastolic blood pressure	3.000000e-27
GCST007095_85	Systolic blood pressure	9.000000e-06
GCST007096_229	Pulse pressure	8.000000e-06
GCST007099_188	Systolic blood pressure	7.000000e-20
GCST008047_9	Platelet count	9.000000e-09
GCST90002401_334	Platelet distribution width	1.000000e-21

EFO canonical traits (5, from GWAS)

EFO ID	Trait name
EFO:0007984	platelet component distribution width
EFO:0006336	diastolic blood pressure
EFO:0006335	systolic blood pressure
EFO:0005763	pulse pressure measurement
EFO:0004309	platelet count

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

21 total (human), top 21 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
dicrotophos	decreases expression	1
pirinixic acid	increases activity, increases expression, affects binding	1
bisphenol A	decreases expression	1
sodium arsenite	decreases expression	1
deguelin	increases expression	1
corosolic acid	increases expression	1
torcetrapib	increases expression	1
Vorinostat	increases expression	1
Vehicle Emissions	decreases methylation	1
Benzo(a)pyrene	affects methylation	1
Caffeine	decreases phosphorylation	1
Doxorubicin	decreases expression	1
Methotrexate	affects response to substance	1
Mitoxantrone	affects response to substance	1
Phenobarbital	affects expression	1
Rotenone	increases expression	1
Smoke	decreases expression	1
Tobacco Smoke Pollution	increases expression	1
Valproic Acid	increases expression	1
Cyclosporine	increases expression	1
Antirheumatic Agents	decreases expression	1

Clinical trials (associated diseases)

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