PRELID3A

Summary

PRELID3A (PRELI domain containing 3A, HGNC:24639) is a protein-coding gene on chromosome 18p11.21, encoding PRELI domain containing protein 3A (Q96N28). In vitro, the TRIAP1:PRELID3A complex mediates the transfer of phosphatidic acid (PA) between liposomes and probably functions as a PA transporter across the mitochondrion intermembrane space.

Enables phosphatidic acid transfer activity. Involved in phospholipid transport. Located in mitochondrion.

Source: NCBI Gene 10650 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 28 total — 1 pathogenic
• MANE Select transcript: NM_001142405

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:24639
Approved symbol	PRELID3A
Name	PRELI domain containing 3A
Location	18p11.21
Locus type	gene with protein product
Status	Approved
Aliases	HFL-EDDG1, FLJ31484
Ensembl gene	ENSG00000141391
Ensembl biotype	protein_coding
OMIM	616545
Entrez	10650

Gene structure

Transcript identifiers

Ensembl transcripts: 9 — 8 protein_coding, 1 nonsense_mediated_decay

ENST00000336990, ENST00000440960, ENST00000587735, ENST00000587862, ENST00000588729, ENST00000589565, ENST00000589952, ENST00000590956, ENST00000592149

RefSeq mRNA: 3 — MANE Select: NM_001142405 NM_001142405, NM_001142406, NM_006553

CCDS: CCDS11860, CCDS77154

Canonical transcript exons

ENST00000440960 — 7 exons

Exon	Start	End
ENSE00001241466	12431150	12432234
ENSE00003551925	12427221	12427323
ENSE00003847883	12407929	12408007
ENSE00003891244	12427041	12427111
ENSE00003891786	12429350	12429436
ENSE00003893212	12420325	12420493
ENSE00003894126	12421540	12421629

Expression profiles

Bgee: expression breadth ubiquitous, 171 present calls, max score 89.87.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 4.3026 / max 108.5483, expressed in 1525 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
169493	4.3026	1525

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
sural nerve	UBERON:0015488	89.87	gold quality
ganglionic eminence	UBERON:0004023	86.98	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	85.73	gold quality
tibial nerve	UBERON:0001323	85.67	gold quality
cortical plate	UBERON:0005343	85.19	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	84.88	gold quality
right frontal lobe	UBERON:0002810	84.33	gold quality
right hemisphere of cerebellum	UBERON:0014890	84.32	gold quality
ventricular zone	UBERON:0003053	84.18	gold quality
cerebellar hemisphere	UBERON:0002245	83.15	gold quality
cerebellar cortex	UBERON:0002129	82.89	gold quality
spinal cord	UBERON:0002240	82.37	gold quality
cingulate cortex	UBERON:0003027	80.79	gold quality
anterior cingulate cortex	UBERON:0009835	80.58	gold quality
cerebellum	UBERON:0002037	80.10	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	79.97	gold quality
Brodmann (1909) area 9	UBERON:0013540	79.86	gold quality
amygdala	UBERON:0001876	79.68	gold quality
body of uterus	UBERON:0009853	79.68	gold quality
popliteal artery	UBERON:0002250	79.23	gold quality
tibial artery	UBERON:0007610	79.23	gold quality
right coronary artery	UBERON:0001625	78.82	gold quality
left uterine tube	UBERON:0001303	78.73	gold quality
nucleus accumbens	UBERON:0001882	78.62	gold quality
stromal cell of endometrium	CL:0002255	78.53	gold quality
aorta	UBERON:0000947	78.44	gold quality
right ovary	UBERON:0002118	78.39	gold quality
left coronary artery	UBERON:0001626	78.19	gold quality
prefrontal cortex	UBERON:0000451	78.05	gold quality
left ovary	UBERON:0002119	77.90	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

Experiment	Marker?	Max mean expression
E-ANND-3	no	2.87

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

32 targeting PRELID3A, 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-3924	100.00	72.09	2394
HSA-MIR-6077	99.99	68.04	2299
HSA-MIR-185-3P	99.95	67.01	1743
HSA-MIR-552-5P	99.93	68.56	1583
HSA-MIR-4492	99.87	68.25	3611
HSA-MIR-1323	99.83	69.89	2471
HSA-MIR-4659A-3P	99.80	72.62	4248
HSA-MIR-4659B-3P	99.80	72.62	4248
HSA-MIR-92A-2-5P	99.75	67.01	2164
HSA-MIR-548O-3P	99.74	69.30	2228
HSA-MIR-4530	99.69	66.47	1509
HSA-MIR-10394-5P	99.65	66.83	1852
HSA-MIR-1205	99.65	66.76	1826
HSA-MIR-6512-3P	99.65	66.07	1468
HSA-MIR-6720-5P	99.65	66.22	1459
HSA-MIR-409-3P	99.50	66.33	1192
HSA-MIR-4316	99.37	65.75	1360
HSA-MIR-7515	99.31	68.22	1795
HSA-MIR-1286	99.09	66.23	1046
HSA-MIR-371A-5P	99.08	66.51	1914
HSA-MIR-3154	98.94	66.55	1455
HSA-MIR-3124-3P	98.87	68.95	2123
HSA-MIR-4717-5P	98.19	67.97	894
HSA-MIR-338-3P	98.14	67.38	1137
HSA-MIR-7154-3P	97.65	65.02	985
HSA-MIR-5586-5P	96.29	68.02	685
HSA-MIR-6813-3P	95.78	63.78	540
HSA-MIR-1237-5P	95.38	62.21	451
HSA-MIR-4488	95.38	62.00	443
HSA-MIR-4697-5P	95.38	61.72	457

Literature-anchored findings (GeneRIF, showing 1)

• crystal structures of free TRIAP1 and TRIAP1-SLMO1 complex reveal how the PRELI domain is chaperoned during import into the intermembrane mitochondrial space; structural resemblance of PRELI-like domain of SLMO1 with that of mammalian phoshatidylinositol transfer proteins suggest they share similar lipid transfer mechanisms (PMID:26071602)

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	prelid3a	ENSDARG00000055288
mus_musculus	Prelid3a	ENSMUSG00000024530
rattus_norvegicus	Prelid3a	ENSRNOG00000017954
drosophila_melanogaster	slmo	FBGN0029161
caenorhabditis_elegans	F15D3.6	WBGENE00008856

Paralogs (3): PRELID3B (ENSG00000101166), PRELID1 (ENSG00000169230), PRELID2 (ENSG00000186314)

Protein

Protein identifiers

PRELI domain containing protein 3A — Q96N28 (reviewed: Q96N28)

Alternative names: Protein slowmo homolog 1

All UniProt accessions (6): Q96N28, K7ELB4, K7ENN4, K7EP78, K7EPM9, K7EQM5

UniProt curated annotations — full annotation on UniProt →

Function. In vitro, the TRIAP1:PRELID3A complex mediates the transfer of phosphatidic acid (PA) between liposomes and probably functions as a PA transporter across the mitochondrion intermembrane space. Phosphatidic acid import is required for cardiolipin (CL) synthesis in the mitochondrial inner membrane.

Subunit / interactions. Interacts with TRIAP1.

Subcellular location. Mitochondrion.

Similarity. Belongs to the slowmo family.

Isoforms (2)

UniProt ID	Names	Canonical?
Q96N28-1	1	yes
Q96N28-2	2

RefSeq proteins (3): NP_001135877, NP_001135878, NP_006544 (=MANE)

Domains & families (InterPro)

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

Pfam: PF04707

UniProt features (18 total): strand 7, helix 3, turn 2, site 2, chain 1, domain 1, splice variant 1, mutagenesis site 1

Structure

Experimental structures (PDB)

2 structures.

PDB	Method	Resolution (Å)
8AG0	X-RAY DIFFRACTION	2.7
4XZV	X-RAY DIFFRACTION	3.58

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q96N28-F1	79.29	0.20

Functional residue map

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

Catalytic / active sites (2): 36 (important for interaction with triap1); 49 (important for interaction with triap1)

Mutagenesis-validated functional residues (1):

Position	Phenotype
36	impairs interaction with triap1.

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

ID	Pathway
R-HSA-6803204	TP53 Regulates Transcription of Genes Involved in Cytochrome C Release

MSigDB gene sets: 145 (showing top): MORF_RAGE, MODULE_52, MORF_FLT1, MORF_MSH3, MODULE_45, MORF_BRCA1, MORF_ATRX, MORF_ESR1, MODULE_16, MORF_RAD51L3, GOBP_ORGANOPHOSPHATE_ESTER_TRANSPORT, MODULE_118, MODULE_379, GOCC_MITOCHONDRIAL_ENVELOPE, MORF_ETV3

GO Biological Process (3): phospholipid transport (GO:0015914), lipid transport (GO:0006869), 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)

Reactome top-level categories

Rollup of top-1 pathways:

Category	Pathways
TP53 Regulates Transcription of Cell Death Genes	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
lipid transport	2
organophosphate ester transport	1
transport	1
lipid localization	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

554 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
PRELID3A	TRIAP1	O43715	624
PRELID3A	AKAIN1	P0CW23	480
PRELID3A	L3MBTL4	Q8NA19	405
PRELID3A	SUSD6	Q92537	398
PRELID3A	ATP23	Q9Y6H3	379
PRELID3A	CCDC183	Q5T5S1	379
PRELID3A	TMEM82	A0PJX8	379
PRELID3A	KLHDC8B	Q8IXV7	374
PRELID3A	SPATA12	Q7Z6I5	371
PRELID3A	TMEM161A	Q9NX61	370
PRELID3A	TMEM200C	A6NKL6	370
PRELID3A	TMEM120B	A0PK00	368
PRELID3A	KIAA2013	Q8IYS2	359
PRELID3A	MOSMO	Q8NHV5	357
PRELID3A	KLHL14	Q9P2G3	356

IntAct

5 interactions, top by confidence:

A	B	Type	Score
TRIAP1	JCHAIN	psi-mi:“MI:0914”(association)	0.530
PRELID3A	TRIAP1	psi-mi:“MI:0914”(association)	0.530
PRELID3A	UBE3A	psi-mi:“MI:0914”(association)	0.350

BioGRID (12): SLMO1 (Two-hybrid), SLMO1 (Co-purification), SLMO1 (Affinity Capture-MS), SLMO1 (Two-hybrid), SLMO1 (Affinity Capture-RNA), SLMO1 (Affinity Capture-RNA), AMN1 (Affinity Capture-MS), SLMO1 (Affinity Capture-MS), KXD1 (Affinity Capture-MS), UBE3A (Affinity Capture-MS), TRIAP1 (Affinity Capture-MS), SLMO1 (Affinity Capture-MS)

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

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

Classification	Count (floor)
Pathogenic	1
Likely pathogenic	0
Uncertain significance	20
Likely benign	1
Benign	0

Top pathogenic / likely-pathogenic (1)

Variant ID	HGVS	Classification
155008	GRCh38/hg38 18p11.22-q11.2(chr18:8779843-24685379)x3	Pathogenic

SpliceAI

1215 predictions. Top by Δscore:

Variant	Effect	Δscore
18:12420320:CGCA:C	acceptor_loss	1.0000
18:12420321:GCA:G	acceptor_loss	1.0000
18:12420322:CAG:C	acceptor_loss	1.0000
18:12420323:A:AG	acceptor_gain	1.0000
18:12420323:A:T	acceptor_loss	1.0000
18:12420324:G:GA	acceptor_gain	1.0000
18:12420324:GC:G	acceptor_gain	1.0000
18:12420324:GCC:G	acceptor_gain	1.0000
18:12420324:GCCA:G	acceptor_gain	1.0000
18:12420324:GCCAC:G	acceptor_gain	1.0000
18:12420480:GCCTC:G	donor_gain	1.0000
18:12420489:GAGCG:G	donor_gain	1.0000
18:12420490:AGCGG:A	donor_loss	1.0000
18:12420491:GCG:G	donor_gain	1.0000
18:12420494:G:GA	donor_loss	1.0000
18:12420494:G:GG	donor_gain	1.0000
18:12420495:T:A	donor_loss	1.0000
18:12421538:A:AG	acceptor_gain	1.0000
18:12421539:G:GG	acceptor_gain	1.0000
18:12421628:AT:A	donor_gain	1.0000
18:12421630:G:GG	donor_gain	1.0000
18:12427320:GAAG:G	donor_gain	1.0000
18:12427324:G:A	donor_loss	1.0000
18:12427325:T:A	donor_loss	1.0000
18:12408280:G:GA	donor_gain	0.9900
18:12420320:C:A	acceptor_gain	0.9900
18:12420496:GA:G	donor_loss	0.9900
18:12421535:TCTA:T	acceptor_loss	0.9900
18:12421537:TAG:T	acceptor_loss	0.9900
18:12421539:G:GC	acceptor_loss	0.9900

AlphaMissense

1130 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
18:12427240:G:C	A128P	0.995
18:12420443:A:C	S51R	0.994
18:12420445:C:A	S51R	0.994
18:12420445:C:G	S51R	0.994
18:12427229:T:C	L124P	0.994
18:12421629:T:A	N97K	0.992
18:12421629:T:G	N97K	0.992
18:12420332:T:A	W14R	0.991
18:12420332:T:C	W14R	0.991
18:12420364:G:C	K24N	0.991
18:12420364:G:T	K24N	0.991
18:12420366:A:G	Y25C	0.991
18:12420449:C:A	R53S	0.991
18:12421582:T:C	S82P	0.991
18:12427066:T:A	V106D	0.991
18:12420334:G:C	W14C	0.990
18:12420334:G:T	W14C	0.990
18:12427083:T:G	Y112D	0.990
18:12420342:T:A	V17D	0.989
18:12427247:T:A	I130N	0.989
18:12427072:A:T	E108V	0.988
18:12429350:G:T	G156W	0.988
18:12420365:T:C	Y25H	0.987
18:12420373:C:A	N27K	0.987
18:12420373:C:G	N27K	0.987
18:12408003:T:C	F10L	0.986
18:12408005:T:A	F10L	0.986
18:12408005:T:G	F10L	0.986
18:12420453:T:C	L54P	0.986
18:12421616:T:C	L93P	0.985

dbSNP variants (sampled 300 via entrez): RS1000204109 (18:12417555 T>G), RS1000237699 (18:12424953 G>T), RS1000349587 (18:12414909 G>C), RS1000413694 (18:12426869 G>A), RS1000498458 (18:12419553 C>T), RS1000609328 (18:12412661 G>C), RS1000627960 (18:12431195 C>A), RS1001284127 (18:12415452 G>A,T), RS1001316633 (18:12415729 C>G,T), RS1001361381 (18:12428525 A>G), RS1001440607 (18:12421626 C>T), RS1001449991 (18:12407804 A>C,G), RS1001827157 (18:12410141 G>A,C), RS1001858442 (18:12415483 C>T), RS1001877041 (18:12421825 T>G)

Disease associations

OMIM: gene MIM:616545 | 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

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

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects cotreatment, decreases expression, affects expression	4
Particulate Matter	increases abundance, increases expression, decreases expression	3
Air Pollutants	increases abundance, increases expression, decreases expression	2
aristolochic acid I	increases expression	1
Esketamine	decreases expression	1
sodium arsenate	increases expression, increases abundance	1
tris(1,3-dichloro-2-propyl)phosphate	affects expression	1
perfluorooctanoic acid	increases expression	1
S-(1,2-dichlorovinyl)cysteine	increases expression	1
perfluorooctane sulfonic acid	increases expression	1
cylindrospermopsin	increases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, decreases expression	1
erucylphospho-N,N,N-trimethylpropylammonium	increases expression	1
abrine	increases expression	1
dorsomorphin	affects cotreatment, decreases expression	1
NSC668394	increases expression	1
Sunitinib	increases expression	1
Leflunomide	decreases expression	1
Acetaminophen	increases expression	1
Arsenic	increases abundance, increases expression	1
Atrazine	increases expression	1
Benzo(a)pyrene	increases methylation	1
Diethylhexyl Phthalate	decreases expression	1
Hydrogen Peroxide	affects expression	1
Phenobarbital	affects expression	1
Smoke	decreases expression	1
Thiram	increases expression	1
Tretinoin	decreases expression	1
Urethane	decreases expression	1
Cyclosporine	decreases expression	1

Clinical trials (associated diseases)

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