PRELID2

Summary

PRELID2 (PRELI domain containing 2, HGNC:28306) is a protein-coding gene on chromosome 5q32, encoding PRELI domain-containing protein 2 (Q8N945).

Predicted to enable phosphatidic acid transfer activity. Predicted to be involved in phospholipid transport. Predicted to be active in mitochondrial intermembrane space.

Source: NCBI Gene 153768 — RefSeq curated summary.

At a glance

• GWAS associations: 7
• Clinical variants (ClinVar): 40 total
• MANE Select transcript: NM_205846

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:28306
Approved symbol	PRELID2
Name	PRELI domain containing 2
Location	5q32
Locus type	gene with protein product
Status	Approved
Aliases	MGC21644, FLJ38376
Ensembl gene	ENSG00000186314
Ensembl biotype	protein_coding
OMIM	620750
Entrez	153768

Gene structure

Transcript identifiers

Ensembl transcripts: 16 — 11 protein_coding, 3 protein_coding_CDS_not_defined, 2 retained_intron

ENST00000334744, ENST00000394450, ENST00000505097, ENST00000505416, ENST00000510259, ENST00000510594, ENST00000511435, ENST00000515161, ENST00000515475, ENST00000683046, ENST00000894033, ENST00000894035, ENST00000894037, ENST00000925513, ENST00000925514, ENST00000941997

RefSeq mRNA: 3 — MANE Select: NM_205846 NM_138492, NM_182960, NM_205846

CCDS: CCDS34261, CCDS34262, CCDS43377

Canonical transcript exons

ENST00000683046 — 7 exons

Exon	Start	End
ENSE00001335392	145819945	145820018
ENSE00001335401	145817894	145818054
ENSE00001342168	145796442	145796547
ENSE00003551492	145823077	145823134
ENSE00003619727	145764931	145765000
ENSE00003920863	145835177	145835342
ENSE00003922165	145756344	145760525

Expression profiles

Bgee: expression breadth ubiquitous, 195 present calls, max score 95.35.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 7.1921 / max 155.8396, expressed in 1616 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
63976	5.6753	1558
63975	1.5168	826

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
oocyte	CL:0000023	95.35	gold quality
secondary oocyte	CL:0000655	95.23	gold quality
colonic mucosa	UBERON:0000317	91.58	gold quality
mucosa of sigmoid colon	UBERON:0004993	91.15	gold quality
mucosa of transverse colon	UBERON:0004991	91.05	gold quality
pancreatic ductal cell	CL:0002079	90.91	gold quality
ileal mucosa	UBERON:0000331	90.82	gold quality
jejunal mucosa	UBERON:0000399	88.56	gold quality
rectum	UBERON:0001052	87.67	gold quality
adrenal tissue	UBERON:0018303	86.92	gold quality
colonic epithelium	UBERON:0000397	85.60	gold quality
calcaneal tendon	UBERON:0003701	84.93	gold quality
duodenum	UBERON:0002114	84.70	gold quality
transverse colon	UBERON:0001157	83.03	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	82.48	gold quality
small intestine	UBERON:0002108	81.43	gold quality
intestine	UBERON:0000160	80.86	gold quality
small intestine Peyer’s patch	UBERON:0003454	80.71	gold quality
large intestine	UBERON:0000059	80.37	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	80.25	gold quality
buccal mucosa cell	CL:0002336	79.99	silver quality
colon	UBERON:0001155	79.89	gold quality
stomach	UBERON:0000945	79.71	gold quality
sperm	CL:0000019	79.39	silver quality
body of pancreas	UBERON:0001150	78.90	gold quality
body of stomach	UBERON:0001161	78.46	gold quality
epithelial cell of pancreas	CL:0000083	78.32	silver quality
pancreas	UBERON:0001264	78.23	gold quality
cartilage tissue	UBERON:0002418	77.72	silver quality
islet of Langerhans	UBERON:0000006	77.21	gold quality

Single-cell (SCXA)

Detected in 3 experiment(s), a significant marker in 3.

Experiment	Marker?	Max mean expression
E-MTAB-11268	yes	2484.84
E-ANND-3	yes	6.76
E-GEOD-137537	yes	4.93

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

189 targeting PRELID2, 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-MIR-340-5P	100.00	72.50	4437
HSA-MIR-3646	100.00	73.56	5283
HSA-MIR-4262	100.00	73.26	3931
HSA-MIR-196A-5P	100.00	68.16	684
HSA-MIR-196B-5P	100.00	68.16	681
HSA-MIR-5692A	100.00	74.40	6850
HSA-MIR-3163	100.00	77.23	8605
HSA-MIR-4533	100.00	69.48	2758
HSA-MIR-574-5P	100.00	66.01	989
HSA-MIR-188-3P	100.00	68.76	1240
HSA-MIR-371B-5P	99.99	75.34	4759
HSA-MIR-4282	99.99	75.36	6408
HSA-MIR-181A-5P	99.99	72.96	2995
HSA-MIR-181B-5P	99.99	72.97	2996
HSA-MIR-181C-5P	99.99	72.95	2996
HSA-MIR-181D-5P	99.99	73.04	2997
HSA-MIR-548AW	99.99	72.57	3559
HSA-MIR-186-5P	99.99	70.83	3707
HSA-MIR-6870-5P	99.99	68.55	2115
HSA-MIR-373-5P	99.98	75.36	4753
HSA-MIR-616-5P	99.98	75.58	4775
HSA-MIR-548N	99.98	71.94	4170
HSA-MIR-12136	99.98	72.81	5713
HSA-MIR-3148	99.97	75.06	6478
HSA-MIR-4723-5P	99.97	68.70	2034
HSA-MIR-5698	99.97	68.49	2029
HSA-MIR-7111-5P	99.97	68.48	2062
HSA-MIR-607	99.97	73.62	5593
HSA-MIR-3658	99.96	73.87	4379

Literature-anchored findings (GeneRIF, showing 1)

• CircPRELID2 functions as a promoter of renal cell carcinoma through the miR-22-3p/ETV1 cascade. (PMID:38730434)

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Prelid2	ENSMUSG00000056671
rattus_norvegicus	Prelid2	ENSRNOG00000067168

Paralogs (3): PRELID3B (ENSG00000101166), PRELID3A (ENSG00000141391), PRELID1 (ENSG00000169230)

Protein

Protein identifiers

PRELI domain-containing protein 2 — Q8N945 (reviewed: Q8N945)

All UniProt accessions (2): D6RAB6, Q8N945

Isoforms (3)

UniProt ID	Names	Canonical?
Q8N945-1	1	yes
Q8N945-2	2
Q8N945-3	3

RefSeq proteins (3): NP_612501, NP_892005, NP_995318* (*=MANE)

Domains & families (InterPro)

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

Pfam: PF04707

UniProt features (6 total): splice variant 3, chain 1, domain 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8N945-F1	87.42	0.58

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 137 (showing top): MENSE_HYPOXIA_UP, GAUSSMANN_MLL_AF4_FUSION_TARGETS_A_UP, GOBP_ORGANOPHOSPHATE_ESTER_TRANSPORT, GOCC_MITOCHONDRIAL_ENVELOPE, PYEON_CANCER_HEAD_AND_NECK_VS_CERVICAL_UP, AACTTT_UNKNOWN, GOBP_PHOSPHOLIPID_TRANSPORT, GOBP_MEMBRANE_ORGANIZATION, BREDEMEYER_RAG_SIGNALING_NOT_VIA_ATM_UP, MARTORIATI_MDM4_TARGETS_FETAL_LIVER_UP, GOBP_LIPID_LOCALIZATION, chr5q32, GOCC_ORGANELLE_ENVELOPE_LUMEN, STAT5A_01, GOMF_LIPID_TRANSPORTER_ACTIVITY

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

GO Molecular Function (1): phosphatidic acid transfer activity (GO:1990050)

GO Cellular Component (1): 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
mitochondrial envelope	1
organelle envelope lumen	1

Protein interactions and networks

STRING

370 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
PRELID2	PRELID1	Q9Y255	681
PRELID2	TRIAP1	O43715	620
PRELID2	G3BP2	Q9UN86	513
PRELID2	TRAPPC9	Q96Q05	493
PRELID2	SH3RF2	Q8TEC5	479
PRELID2	GRXCR2	A6NFK2	478
PRELID2	COL22A1	Q8NFW1	466
PRELID2	PLAC8L1	A1L4L8	404
PRELID2	NKAIN3	Q8N8D7	393
PRELID2	DTWD1	Q8N5C7	391
PRELID2	FAM234B	A2RU67	385
PRELID2	STK32A	Q8WU08	382
PRELID2	SMIM5	Q71RC9	371
PRELID2	TEX2	Q8IWB9	354
PRELID2	HMHB1	O97980	353

IntAct

3 interactions, top by confidence:

A	B	Type	Score
PRELID2	TP73	psi-mi:“MI:0914”(association)	0.350
KLHL22	TRAV18	psi-mi:“MI:0914”(association)	0.350

BioGRID (18): PRELID2 (Synthetic Lethality), KIF11 (Affinity Capture-MS), TP73 (Affinity Capture-MS), BRCA2 (Affinity Capture-MS), HAUS8 (Affinity Capture-MS), MLF1 (Affinity Capture-MS), WDR62 (Affinity Capture-MS), NCOA4 (Affinity Capture-MS), BUB1 (Affinity Capture-MS), EXPH5 (Affinity Capture-MS), ALMS1 (Affinity Capture-MS), FAM83D (Affinity Capture-MS), BORA (Affinity Capture-MS), CDK5RAP2 (Affinity Capture-MS), HAUS6 (Affinity Capture-MS)

ESM2 similar proteins: A1A4M6, A2AGL3, B3DLA6, O65502, P14893, P26149, P27365, P42694, P48738, P48739, P53811, P53812, Q00169, Q0P5D8, Q0VBB0, Q28C34, Q2HJ54, Q32KN9, Q4R7G8, Q53H12, Q5BKH5, Q5F477, Q5IFP1, Q5R6F0, Q5R8P9, Q62878, Q6DFV5, Q6NRD0, Q6NTS7, Q6TV19, Q7RTV5, Q7ZUV0, Q7ZYD9, Q8CA95, Q8IX04, Q8N945, Q8R107, Q8VCM5, Q8VHQ9, Q8W4D4

Diamond homologs: Q0VBB0, Q5BKH5, Q6NTS7, Q8N945, O59707, Q54G07

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	27
Likely benign	1
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1889 predictions. Top by Δscore:

Variant	Effect	Δscore
5:145817888:TCTTA:T	donor_loss	1.0000
5:145817890:TTA:T	donor_loss	1.0000
5:145817892:A:AC	donor_gain	1.0000
5:145817892:A:AG	donor_loss	1.0000
5:145817893:C:CC	donor_gain	1.0000
5:145817893:C:CG	donor_loss	1.0000
5:145817893:CCA:C	donor_gain	1.0000
5:145817915:T:A	donor_gain	1.0000
5:145817933:T:TA	donor_gain	1.0000
5:145818050:CTCAC:C	acceptor_gain	1.0000
5:145818051:TCAC:T	acceptor_gain	1.0000
5:145818052:CAC:C	acceptor_gain	1.0000
5:145818052:CACC:C	acceptor_gain	1.0000
5:145818053:ACC:A	acceptor_loss	1.0000
5:145818055:CTGT:C	acceptor_loss	1.0000
5:145818056:T:C	acceptor_loss	1.0000
5:145819940:CTTA:C	donor_loss	1.0000
5:145819941:TTA:T	donor_loss	1.0000
5:145819942:TA:T	donor_loss	1.0000
5:145819943:A:AC	donor_gain	1.0000
5:145819943:AC:A	donor_gain	1.0000
5:145819943:ACCTT:A	donor_gain	1.0000
5:145819944:C:CC	donor_gain	1.0000
5:145819944:C:CG	donor_loss	1.0000
5:145819944:CC:C	donor_gain	1.0000
5:145819944:CCTT:C	donor_gain	1.0000
5:145819944:CCTTC:C	donor_gain	1.0000
5:145819947:T:A	donor_gain	1.0000
5:145820016:CAT:C	acceptor_gain	1.0000
5:145820017:AT:A	acceptor_gain	1.0000

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000001280 (5:145353496 T>C), RS1000007813 (5:145668618 T>G), RS1000009510 (5:145833832 A>G), RS1000011553 (5:145488985 C>A,T), RS1000016150 (5:145646437 C>T), RS1000027025 (5:145493590 GTC>G), RS1000033052 (5:145282518 T>C), RS1000039751 (5:145526528 TG>T), RS1000046573 (5:145322676 A>G), RS1000049676 (5:145608498 C>T), RS1000058794 (5:145769274 A>C,G), RS1000059814 (5:145446217 T>C), RS1000071151 (5:145295007 A>G), RS1000090967 (5:145568585 T>C), RS1000091842 (5:145288294 T>C)

Disease associations

OMIM: gene MIM:620750 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

7 associations (top):

Study	Trait	p-value
GCST003943_6	Hepcidin levels	7.000000e-07
GCST003944_42	Hepcidin/ferritin ratio	8.000000e-08
GCST003992_13	Photic sneeze reflex	4.000000e-09
GCST008660_3	Lung function in never smokers (high FEV1 vs average FEV1)	2.000000e-07
GCST009173_1	Response to (pegylated) interferon in HBeAG-positive hepatitis B	3.000000e-06
GCST010244_183	Triglyceride levels	2.000000e-08
GCST90093090_5	DHEAS levels	9.000000e-06

EFO canonical traits (6, from GWAS)

EFO ID	Trait name
EFO:0007901	hepcidin:ferritin ratio
EFO:0007887	autosomal dominant compelling helio-ophthalmic outburst syndrome
EFO:0004314	forced expiratory volume
EFO:0007859	response to interferon
EFO:0004530	triglyceride measurement
EFO:0007001	dehydroepiandrosterone sulphate measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

25 total (human), top 25 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	increases expression, affects expression	2
aristolochic acid I	decreases expression	1
dicrotophos	decreases expression	1
propionaldehyde	decreases expression	1
pirinixic acid	affects binding, decreases expression, increases activity	1
beta-lapachone	decreases expression	1
arsenite	affects binding, increases reaction	1
tris(1,3-dichloro-2-propyl)phosphate	decreases expression	1
sodium arsenite	decreases expression	1
butyraldehyde	decreases expression	1
potassium chromate(VI)	affects cotreatment, decreases expression	1
epigallocatechin gallate	affects cotreatment, decreases expression	1
K 7174	decreases expression	1
abrine	decreases expression	1
Acetaminophen	decreases expression	1
Benzo(a)pyrene	affects methylation	1
Diethylhexyl Phthalate	decreases expression	1
Estradiol	increases expression	1
Oxygen	increases expression	1
Quercetin	decreases expression	1
Thimerosal	decreases expression	1
Tobacco Smoke Pollution	decreases expression	1
Tretinoin	decreases expression	1
Cyclosporine	affects expression	1
Cadmium Chloride	increases expression	1

Clinical trials (associated diseases)

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