LDLRAD1

Summary

LDLRAD1 (low density lipoprotein receptor class A domain containing 1, HGNC:32069) is a protein-coding gene on chromosome 1p32.3, encoding Low-density lipoprotein receptor class A domain-containing protein 1 (Q5T700).

Predicted to be involved in vesicle-mediated transport. Predicted to be located in membrane.

Source: NCBI Gene 388633 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 37 total
• MANE Select transcript: NM_001010978

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:32069
Approved symbol	LDLRAD1
Name	low density lipoprotein receptor class A domain containing 1
Location	1p32.3
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000203985
Ensembl biotype	protein_coding
Entrez	388633

Gene structure

Transcript identifiers

Ensembl transcripts: 5 — 5 protein_coding

ENST00000371360, ENST00000371362, ENST00000420619, ENST00000545928, ENST00000882503

RefSeq mRNA: 5 — MANE Select: NM_001010978 NM_001010978, NM_001276392, NM_001276393, NM_001276394, NM_001276395

CCDS: CCDS30725, CCDS60145, CCDS60146, CCDS60147

Canonical transcript exons

ENST00000371360 — 6 exons

Exon	Start	End
ENSE00001455008	54007298	54009130
ENSE00001455009	54012143	54012280
ENSE00001455010	54014236	54014364
ENSE00001455013	54010282	54010410
ENSE00001455014	54017376	54017427
ENSE00003739792	54018092	54018186

Expression profiles

Bgee: expression breadth broad, 51 present calls, max score 99.05.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.2090 / max 56.4410, expressed in 51 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
12445	0.1104	39
12444	0.0986	33

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
right uterine tube	UBERON:0001302	99.05	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	92.57	gold quality
fallopian tube	UBERON:0003889	83.92	gold quality
right lung	UBERON:0002167	71.89	gold quality
adrenal tissue	UBERON:0018303	67.69	gold quality
left uterine tube	UBERON:0001303	64.48	gold quality
left adrenal gland	UBERON:0001234	61.01	gold quality
minor salivary gland	UBERON:0001830	60.23	gold quality
lung	UBERON:0002048	60.11	gold quality
adrenal gland	UBERON:0002369	60.01	gold quality
right adrenal gland	UBERON:0001233	60.00	gold quality
saliva-secreting gland	UBERON:0001044	59.36	gold quality
gall bladder	UBERON:0002110	59.27	gold quality
endometrium	UBERON:0001295	59.21	gold quality
left adrenal gland cortex	UBERON:0035825	58.92	gold quality
right adrenal gland cortex	UBERON:0035827	58.25	gold quality
islet of Langerhans	UBERON:0000006	58.17	gold quality
upper lobe of left lung	UBERON:0008952	56.66	gold quality
endocervix	UBERON:0000458	55.65	gold quality
lower esophagus mucosa	UBERON:0035834	54.80	gold quality
esophagus mucosa	UBERON:0002469	49.75	gold quality
prostate gland	UBERON:0002367	47.88	gold quality
uterine cervix	UBERON:0000002	46.37	gold quality
pancreas	UBERON:0001264	44.30	gold quality
rectum	UBERON:0001052	42.99	gold quality
sural nerve	UBERON:0015488	42.52	gold quality
monocyte	CL:0000576	42.50	gold quality
leukocyte	CL:0000738	41.71	gold quality
esophagus	UBERON:0001043	41.45	gold quality
ventricular zone	UBERON:0003053	40.05	gold quality

Single-cell (SCXA)

Detected in 4 experiment(s), a significant marker in 4.

Experiment	Marker?	Max mean expression
E-CURD-114	yes	64.04
E-MTAB-10287	yes	24.87
E-GEOD-130148	yes	12.51
E-ANND-3	no	0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

72 targeting LDLRAD1, 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-12118	100.00	65.88	1270
HSA-MIR-3173-3P	99.98	66.49	1217
HSA-MIR-6891-5P	99.98	66.53	1372
HSA-MIR-4775	99.98	75.00	6394
HSA-MIR-23B-5P	99.98	66.07	587
HSA-MIR-8068	99.98	73.85	2376
HSA-MIR-548AA	99.96	70.64	3753
HSA-MIR-548AP-3P	99.96	70.64	3753
HSA-MIR-548T-3P	99.96	70.64	3753
HSA-MIR-4725-3P	99.96	69.53	2520
HSA-MIR-6780B-5P	99.96	69.60	2562
HSA-MIR-23A-5P	99.94	65.39	468
HSA-MIR-4731-5P	99.89	67.23	2537
HSA-MIR-153-5P	99.89	73.86	6317
HSA-MIR-6783-3P	99.89	67.92	2059
HSA-MIR-1343-3P	99.89	66.78	1815
HSA-MIR-30A-3P	99.87	69.74	2928
HSA-MIR-30D-3P	99.87	69.92	2917
HSA-MIR-30E-3P	99.87	69.68	2942
HSA-MIR-6079	99.84	68.54	1170
HSA-MIR-765	99.84	68.24	2442
HSA-MIR-130B-5P	99.83	68.50	1888
HSA-MIR-4495	99.82	72.08	3080
HSA-MIR-3934-3P	99.76	65.51	1351
HSA-MIR-11181-3P	99.75	66.38	2205
HSA-MIR-148A-3P	99.74	73.77	1700
HSA-MIR-148B-3P	99.74	73.75	1700
HSA-MIR-152-3P	99.74	73.75	1703
HSA-MIR-4524A-3P	99.72	66.85	2406
HSA-MIR-4306	99.72	70.50	3630

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
mus_musculus	Ldlrad1	ENSMUSG00000070877
rattus_norvegicus	Ldlrad1	ENSRNOG00000037795
drosophila_melanogaster	loaf	FBGN0036202

Protein

Protein identifiers

Low-density lipoprotein receptor class A domain-containing protein 1 — Q5T700 (reviewed: Q5T700)

All UniProt accessions (1): Q5T700

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Membrane.

Similarity. Belongs to the LDLR family.

Isoforms (4)

UniProt ID	Names	Canonical?
Q5T700-1	1	yes
Q5T700-2	2
Q5T700-3	3
Q5T700-4	4

RefSeq proteins (5): NP_001010978, NP_001263321, NP_001263322, NP_001263323, NP_001263324 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR002172	LDrepeatLR_classA_rpt	Repeat
IPR036055	LDL_receptor-like_sf	Homologous_superfamily
IPR050685	LDLR	Family
IPR057430	LDLRAD1_C	Domain

Pfam: PF00057, PF25241

UniProt features (14 total): disulfide bond 6, splice variant 3, domain 3, chain 1, transmembrane region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q5T700-F1	83.46	0.67

Functional residue map

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

Disulfide bonds (6): 170–193, 72–89, 83–102, 96–113, 141–160, 163–180

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 20 (showing top): GOBP_VESICLE_MEDIATED_TRANSPORT, GSE13762_CTRL_VS_125_VITAMIND_DAY12_DC_DN, MIR548AA_MIR548AP_3P_MIR548T_3P, MIR3059_5P, MIR892C_5P, MIR4524A_3P, MIR504_3P, MIR6079, GAO_ESOPHAGUS_25W_C1_CILIATED_EPITHELIAL_CELLS, DURANTE_ADULT_OLFACTORY_NEUROEPITHELIUM_RESPIRATORY_CILIATED_CELLS, DESCARTES_MAIN_FETAL_CILIATED_EPITHELIAL_CELLS, DESCARTES_FETAL_LUNG_CILIATED_EPITHELIAL_CELLS, DESCARTES_FETAL_STOMACH_CILIATED_EPITHELIAL_CELLS, TRAVAGLINI_LUNG_CILIATED_CELL, TRAVAGLINI_LUNG_PROXIMAL_CILIATED_CELL

GO Biological Process (1): vesicle-mediated transport (GO:0016192)

GO Molecular Function (1): protein binding (GO:0005515)

GO Cellular Component (1): membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
transport	1
cellular process	1
binding	1
cellular anatomical structure	1

Protein interactions and networks

STRING

2534 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
LDLRAD1	SHISA8	B8ZZ34	580
LDLRAD1	CDHR3	Q6ZTQ4	556
LDLRAD1	SNTN	A6NMZ2	543
LDLRAD1	OR10S1	Q8NGN2	504
LDLRAD1	MCIDAS	D6RGH6	469
LDLRAD1	MSANTD1	Q6ZTZ1	447
LDLRAD1	MROH7	Q68CQ1	434
LDLRAD1	GAS2L2	Q8NHY3	430
LDLRAD1	ANKS4B	Q8N8V4	426
LDLRAD1	CFAP157	Q5JU67	418
LDLRAD1	CFAP58	Q5T655	416
LDLRAD1	TCEANC2	Q96MN5	407
LDLRAD1	CFAP53	Q96M91	402
LDLRAD1	SLCO1B7	G3V0H7	395
LDLRAD1	TMEM212	A6NML5	394

IntAct

153 interactions, top by confidence:

A	B	Type	Score
LDLRAD1	TMEM218	psi-mi:“MI:0915”(physical association)	0.830
TMEM218	LDLRAD1	psi-mi:“MI:0915”(physical association)	0.830
MAL	LDLRAD1	psi-mi:“MI:0915”(physical association)	0.780
MALL	LDLRAD1	psi-mi:“MI:0915”(physical association)	0.780
LDLRAD1	OLFM4	psi-mi:“MI:0915”(physical association)	0.780
LDLRAD1	TMEM190	psi-mi:“MI:0915”(physical association)	0.780
ADGRG7	LDLRAD1	psi-mi:“MI:0915”(physical association)	0.780
LDLRAD1	TMEM147	psi-mi:“MI:0915”(physical association)	0.780
MARCHF2	LDLRAD1	psi-mi:“MI:0915”(physical association)	0.780
LDLRAD1	VTI1B	psi-mi:“MI:0915”(physical association)	0.780
LDLRAD1	MALL	psi-mi:“MI:0915”(physical association)	0.780
OLFM4	LDLRAD1	psi-mi:“MI:0915”(physical association)	0.780
LDLRAD1	ADGRG7	psi-mi:“MI:0915”(physical association)	0.780
LDLRAD1	MARCHF2	psi-mi:“MI:0915”(physical association)	0.780
VTI1B	LDLRAD1	psi-mi:“MI:0915”(physical association)	0.780
TMEM190	LDLRAD1	psi-mi:“MI:0915”(physical association)	0.780
TMEM147	LDLRAD1	psi-mi:“MI:0915”(physical association)	0.780

BioGRID (211): LDLRAD1 (Two-hybrid), LDLRAD1 (Two-hybrid), LDLRAD1 (Two-hybrid), LDLRAD1 (Two-hybrid), LDLRAD1 (Two-hybrid), LDLRAD1 (Two-hybrid), LDLRAD1 (Two-hybrid), LDLRAD1 (Two-hybrid), LDLRAD1 (Two-hybrid), LDLRAD1 (Two-hybrid), LDLRAD1 (Two-hybrid), LDLRAD1 (Two-hybrid), LDLRAD1 (Two-hybrid), LDLRAD1 (Two-hybrid), LDLRAD1 (Two-hybrid)

ESM2 similar proteins: A6NCL2, D3ZTT2, O19131, O46655, O70280, P01177, P01178, P01179, P01180, P01183, P01185, P01186, P03973, P13389, P19438, P22298, P22934, P25118, P35454, P35455, P50555, P58658, P58659, Q02509, Q14AE4, Q32LD3, Q3URS3, Q5T700, Q68US5, Q6UWE3, Q6UWL2, Q6V9X0, Q6WN34, Q76LW6, Q86Y78, Q8BPP5, Q8BVP6, Q8N6Q3, Q8VEA6, Q8WXA2

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	27
Likely benign	4
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1285 predictions. Top by Δscore:

Variant	Effect	Δscore
1:54010276:CCCTA:C	donor_loss	0.9800
1:54010277:CCTA:C	donor_loss	0.9800
1:54010278:CTAC:C	donor_loss	0.9800
1:54010279:TACCT:T	donor_loss	0.9800
1:54010280:A:AG	donor_loss	0.9800
1:54010281:C:CG	donor_loss	0.9800
1:54010408:CTC:C	acceptor_gain	0.9800
1:54010411:C:CC	acceptor_gain	0.9800
1:54009127:GTTAC:G	acceptor_loss	0.9700
1:54009128:TTA:T	acceptor_gain	0.9700
1:54009128:TTAC:T	acceptor_loss	0.9700
1:54009130:ACT:A	acceptor_loss	0.9700
1:54009131:C:CC	acceptor_gain	0.9700
1:54009131:C:T	acceptor_loss	0.9700
1:54009132:T:C	acceptor_loss	0.9700
1:54010411:CTGT:C	acceptor_loss	0.9700
1:54010412:T:G	acceptor_loss	0.9700
1:54012141:A:AC	donor_gain	0.9700
1:54012142:C:CC	donor_gain	0.9700
1:54012142:CGG:C	donor_gain	0.9700
1:54009104:C:T	acceptor_gain	0.9600
1:54009126:AGTTA:A	acceptor_gain	0.9600
1:54009127:GTTA:G	acceptor_gain	0.9600
1:54009129:TA:T	acceptor_gain	0.9600
1:54012142:CGGCA:C	donor_gain	0.9600
1:54009110:C:CT	acceptor_gain	0.9500
1:54009148:A:T	acceptor_gain	0.9500
1:54010282:C:A	donor_loss	0.9500
1:54009548:A:AC	donor_gain	0.9400
1:54009549:C:CC	donor_gain	0.9400

AlphaMissense

1330 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
1:54012240:G:C	F81L	0.985
1:54012240:G:T	F81L	0.985
1:54012242:A:G	F81L	0.985
1:54012241:A:C	F81C	0.983
1:54009096:C:A	W168C	0.982
1:54009096:C:G	W168C	0.982
1:54010311:C:G	C147S	0.976
1:54010312:A:T	C147S	0.976
1:54010329:C:G	C141S	0.976
1:54010330:A:T	C141S	0.976
1:54009022:C:G	C193S	0.975
1:54009023:A:T	C193S	0.975
1:54009021:G:C	C193W	0.969
1:54012196:C:G	C96S	0.969
1:54012197:A:T	C96S	0.969
1:54012241:A:G	F81S	0.967
1:54009022:C:T	C193Y	0.962
1:54010368:C:G	C128S	0.961
1:54010369:A:T	C128S	0.961
1:54010311:C:T	C147Y	0.958
1:54009091:C:G	C170S	0.957
1:54009092:A:T	C170S	0.957
1:54012235:C:G	C83S	0.955
1:54012236:A:T	C83S	0.955
1:54010368:C:T	C128Y	0.953
1:54009012:C:A	W196C	0.951
1:54009012:C:G	W196C	0.951
1:54010297:C:G	D152H	0.949
1:54010311:C:A	C147F	0.947
1:54012145:C:G	C113S	0.947

dbSNP variants (sampled 300 via entrez): RS1000241137 (1:54013735 T>C), RS1000419486 (1:54008851 C>A,T), RS1000464144 (1:54008021 A>T), RS1000651175 (1:54014010 A>G), RS1000707575 (1:54019904 A>G,T), RS1001426403 (1:54010048 A>G,T), RS1001463747 (1:54016602 C>A,T), RS1002037552 (1:54015134 C>A,G,T), RS1002311461 (1:54011185 C>T), RS1002587268 (1:54017086 G>T), RS1002849826 (1:54014849 C>G), RS1003056600 (1:54009708 T>C), RS1003074824 (1:54009397 G>A), RS1003134214 (1:54015198 A>G), RS1003185179 (1:54013827 G>C)

Disease associations

OMIM: gene `` | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

1 associations (top):

Study	Trait	p-value
GCST002778_2	Parkinson disease and lewy body pathology	6.000000e-08

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

17 total (human), top 17 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Tobacco Smoke Pollution	affects expression, decreases expression	2
OTX015	decreases expression	1
sotorasib	affects cotreatment, decreases expression	1
sodium arsenite	decreases expression	1
CGP 52608	affects binding, increases reaction	1
nutlin 3	affects cotreatment, increases expression	1
abrine	decreases expression	1
trametinib	affects cotreatment, decreases expression	1
NVP-BKM120	affects cotreatment, decreases expression	1
Arsenic Trioxide	increases expression	1
Acetaminophen	increases expression	1
Air Pollutants	increases abundance, increases expression	1
Benzo(a)pyrene	affects methylation	1
Dactinomycin	affects cotreatment, increases expression	1
Silicon Dioxide	decreases expression	1
Smoke	increases abundance, increases expression	1
Urethane	decreases expression	1

Clinical trials (associated diseases)

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