CLUL1

Summary

CLUL1 (clusterin like 1, HGNC:2096) is a protein-coding gene on chromosome 18p11.32, encoding Clusterin-like protein 1 (Q15846).

Predicted to enable misfolded protein binding activity. Predicted to be located in extracellular region. Predicted to be active in extracellular space and nucleus.

Source: NCBI Gene 27098 — RefSeq curated summary.

At a glance

• GWAS associations: 2
• Clinical variants (ClinVar): 75 total — 1 pathogenic
• MANE Select transcript: NM_001393344

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:2096
Approved symbol	CLUL1
Name	clusterin like 1
Location	18p11.32
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000079101
Ensembl biotype	protein_coding
OMIM	616990
Entrez	27098

Gene structure

Transcript identifiers

Ensembl transcripts: 13 — 8 protein_coding, 4 protein_coding_CDS_not_defined, 1 retained_intron

ENST00000338387, ENST00000400606, ENST00000540035, ENST00000579443, ENST00000579494, ENST00000579912, ENST00000580436, ENST00000581619, ENST00000582020, ENST00000584046, ENST00000584370, ENST00000585155, ENST00000692774

RefSeq mRNA: 10 — MANE Select: NM_001393344 NM_001289036, NM_001318522, NM_001375492, NM_001393344, NM_001393345, NM_001393346, NM_001393347, NM_001393348, NM_014410, NM_199167

CCDS: CCDS42405

Canonical transcript exons

ENST00000692774 — 10 exons

Exon	Start	End
ENSE00001208384	641327	641541
ENSE00001230733	644910	645097
ENSE00001230744	633298	633435
ENSE00001230752	627097	627529
ENSE00002698264	649898	650182
ENSE00002700165	596988	597129
ENSE00003471021	606978	607099
ENSE00003486455	617988	618106
ENSE00003529187	619213	619361
ENSE00003661277	624865	625032

Expression profiles

Bgee: expression breadth ubiquitous, 175 present calls, max score 84.70.

FANTOM5 (CAGE): breadth broad, TPM avg 0.5143 / max 86.3404, expressed in 189 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter ID	TPM avg	Samples expressed
169053	0.3873	183
169055	0.0834	7
169056	0.0309	4
169054	0.0127	4

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
pigmented layer of retina	UBERON:0001782	84.70	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	83.30	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	80.02	gold quality
choroid plexus epithelium	UBERON:0003911	79.89	gold quality
buccal mucosa cell	CL:0002336	78.46	gold quality
prefrontal cortex	UBERON:0000451	74.41	gold quality
adenohypophysis	UBERON:0002196	73.13	gold quality
islet of Langerhans	UBERON:0000006	72.80	gold quality
left lobe of thyroid gland	UBERON:0001120	72.80	gold quality
thyroid gland	UBERON:0002046	71.95	gold quality
right lobe of thyroid gland	UBERON:0001119	71.72	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	71.43	gold quality
Brodmann (1909) area 9	UBERON:0013540	71.17	gold quality
pituitary gland	UBERON:0000007	70.53	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	70.43	gold quality
right frontal lobe	UBERON:0002810	70.29	gold quality
secondary oocyte	CL:0000655	70.11	silver quality
cortical plate	UBERON:0005343	69.88	gold quality
prostate gland	UBERON:0002367	69.78	gold quality
frontal cortex	UBERON:0001870	69.24	gold quality
anterior cingulate cortex	UBERON:0009835	69.14	gold quality
cingulate cortex	UBERON:0003027	69.06	gold quality
cerebellar cortex	UBERON:0002129	69.03	gold quality
cerebellar hemisphere	UBERON:0002245	68.95	gold quality
hypothalamus	UBERON:0001898	68.94	gold quality
neocortex	UBERON:0001950	68.86	gold quality
spinal cord	UBERON:0002240	68.41	gold quality
right hemisphere of cerebellum	UBERON:0014890	68.01	gold quality
cerebral cortex	UBERON:0000956	67.48	gold quality
cerebellum	UBERON:0002037	67.47	gold quality

Single-cell (SCXA)

Detected in 4 experiment(s), a significant marker in 2.

Experiment	Marker?	Max mean expression
E-MTAB-7316	yes	1702.99
E-GEOD-98556	yes	1601.27
E-MTAB-8060	no	104.73
E-ANND-3	no	0.00

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): MYC

miRNA regulators (miRDB)

34 targeting CLUL1, 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-190A-3P	100.00	80.35	5520
HSA-MIR-5011-5P	100.00	83.46	5820
HSA-MIR-12118	100.00	65.88	1270
HSA-MIR-6891-5P	99.98	66.53	1372
HSA-MIR-3173-3P	99.98	66.49	1217
HSA-MIR-205-3P	99.92	69.92	3165
HSA-MIR-454-3P	99.91	74.01	1925
HSA-MIR-10527-5P	99.91	72.28	3754
HSA-MIR-130A-3P	99.90	73.31	1861
HSA-MIR-130B-3P	99.90	73.27	1850
HSA-MIR-301A-3P	99.90	73.15	1839
HSA-MIR-301B-3P	99.90	73.19	1836
HSA-MIR-3666	99.90	73.24	1833
HSA-MIR-4295	99.90	73.11	1838
HSA-MIR-380-3P	99.89	70.18	1978
HSA-MIR-7856-5P	99.75	69.99	2901
HSA-MIR-519A-3P	99.67	71.67	1868
HSA-MIR-519B-3P	99.67	71.67	1868
HSA-MIR-519C-3P	99.67	71.67	1870
HSA-MIR-2053	99.57	69.15	1635
HSA-MIR-10524-5P	99.05	66.08	963
HSA-MIR-4709-3P	98.88	68.04	1594
HSA-MIR-3074-5P	98.82	66.56	1414
HSA-MIR-501-5P	98.77	68.88	1328
HSA-MIR-4272	98.76	68.74	1810
HSA-MIR-496	98.66	69.80	931
HSA-MIR-4511	98.32	67.97	1500
HSA-MIR-138-1-3P	98.25	67.89	867
HSA-MIR-1243	97.07	65.44	719
HSA-MIR-3674	97.01	68.86	1171

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
danio_rerio	clul1	ENSDARG00000055595
rattus_norvegicus	Clul1	ENSRNOG00000059237

Paralogs (1): CLU (ENSG00000120885)

Protein

Protein identifiers

Clusterin-like protein 1 — Q15846 (reviewed: Q15846)

Alternative names: Retinal-specific clusterin-like protein

All UniProt accessions (5): Q15846, F5GWQ8, J3QKW8, R4GN76, R4GN95

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Secreted.

Similarity. Belongs to the clusterin family.

RefSeq proteins (10): NP_001275965, NP_001305451, NP_001362421, NP_001380273, NP_001380274, NP_001380275, NP_001380276, NP_001380277, NP_055225, NP_954636 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR000753	Clusterin-like	Family
IPR016014	Clusterin_N	Domain
IPR016015	Clusterin_C	Domain

Pfam: PF01093

UniProt features (14 total): glycosylation site 6, disulfide bond 5, signal peptide 1, chain 1, coiled-coil region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q15846-F1	65.03	0.15

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 (5): 116–325, 119–322, 124–315, 131–305, 105–333

Glycosylation sites (6): 196, 257, 311, 351, 412, 431

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 47 (showing top): RIZKI_TUMOR_INVASIVENESS_3D_DN, MODULE_113, DANG_BOUND_BY_MYC, GOMF_MISFOLDED_PROTEIN_BINDING, KRAS.300_UP.V1_UP, KRAS.600_UP.V1_UP, HMGA1_TARGET_GENES, MAFG_TARGET_GENES, SRSF9_TARGET_GENES, THRA_TARGET_GENES, TOP2B_TARGET_GENES, ZNF664_TARGET_GENES, ZNF8_TARGET_GENES, MIR7856_5P, MIR2053

GO Biological Process (0):

GO Molecular Function (1): misfolded protein binding (GO:0051787)

GO Cellular Component (3): obsolete extracellular space (GO:0005615), nucleus (GO:0005634), extracellular region (GO:0005576)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
protein binding	1
intracellular membrane-bounded organelle	1
cellular anatomical structure	1

Protein interactions and networks

STRING

807 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CLUL1	ENOSF1	Q7L5Y1	621
CLUL1	AKAIN1	P0CW23	609
CLUL1	CETN1	Q12798	540
CLUL1	MYOM1	P52179	518
CLUL1	COLEC12	Q5KU26	509
CLUL1	THOC1	Q96FV9	507
CLUL1	LPIN2	Q92539	505
CLUL1	ZBTB14	O43829	477
CLUL1	EMILIN2	Q9BXX0	447
CLUL1	RBP3	P10745	423
CLUL1	MYL12A	P19105	419
CLUL1	MYL12B	O14950	407
CLUL1	SMCHD1	A6NHR9	400
CLUL1	ADCYAP1	P18509	400
CLUL1	DLGAP1	P78335	398

IntAct

1 interactions, top by confidence:

A	B	Type	Score
	LECT2	psi-mi:“MI:0915”(physical association)	0.400

BioGRID (2): CLUL1 (Affinity Capture-MS), EEA1 (Cross-Linking-MS (XL-MS))

ESM2 similar proteins: A0A1B0GVN3, A0JPP4, A4H257, A4H258, A4H260, A6NKB5, A6QLI2, A7WNB0, B9EKR1, F5HB98, O75969, O77797, P11450, P15522, P33735, P33736, P47867, P61110, P80195, P81447, Q00997, Q15846, Q1XI86, Q2LCV6, Q30KK0, Q32KL7, Q32MG2, Q3ZRW6, Q3ZRW7, Q49AJ0, Q569E4, Q5RBQ2, Q5RII3, Q5XI62, Q641I1, Q6AXV6, Q6UW49, Q8JSZ3, Q8TAL5, Q95KN1

Diamond homologs: P05371, P10909, P14018, P14683, P17697, P25473, Q06890, Q15846, Q29482, Q29549, Q3ZRW6, Q3ZRW7, Q3ZRW9, Q9XSC5, Q95KN1

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	1
Likely pathogenic	0
Uncertain significance	62
Likely benign	2
Benign	0

Top pathogenic / likely-pathogenic (1)

Variant ID	HGVS	Classification
3062373	GRCh37/hg19 18p11.32-11.21(chr18:136227-15157836)x3	Pathogenic

SpliceAI

2057 predictions. Top by Δscore:

Variant	Effect	Δscore
18:618102:GAAGA:G	donor_gain	1.0000
18:618105:GA:G	donor_gain	1.0000
18:618107:G:GG	donor_gain	1.0000
18:619357:AGCAG:A	donor_loss	1.0000
18:619358:GCAG:G	donor_gain	1.0000
18:619359:CAGGT:C	donor_loss	1.0000
18:619360:AGGTA:A	donor_loss	1.0000
18:619361:GG:G	donor_loss	1.0000
18:619363:T:A	donor_loss	1.0000
18:625029:TAAGG:T	donor_loss	1.0000
18:625031:AGGT:A	donor_loss	1.0000
18:633296:A:AG	acceptor_gain	1.0000
18:633297:G:GA	acceptor_gain	1.0000
18:644909:GGTA:G	acceptor_gain	1.0000
18:597127:CAGG:C	donor_loss	0.9900
18:597131:T:G	donor_loss	0.9900
18:614560:GC:G	donor_gain	0.9900
18:617986:A:AG	acceptor_gain	0.9900
18:617987:G:GA	acceptor_gain	0.9900
18:618091:A:AG	donor_gain	0.9900
18:618092:G:GG	donor_gain	0.9900
18:618104:AGA:A	donor_gain	0.9900
18:618105:GAG:G	donor_gain	0.9900
18:619208:TTTA:T	acceptor_loss	0.9900
18:619211:A:AG	acceptor_gain	0.9900
18:619211:AGGT:A	acceptor_loss	0.9900
18:619212:G:GC	acceptor_loss	0.9900
18:619212:G:GG	acceptor_gain	0.9900
18:619212:G:T	acceptor_gain	0.9900
18:619359:C:T	donor_gain	0.9900

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000025117 (18:621793 G>A), RS1000039245 (18:646474 C>G), RS1000040792 (18:642361 G>A), RS1000107593 (18:648132 A>C), RS1000200696 (18:615615 A>G), RS1000217760 (18:639917 G>C), RS1000312968 (18:639750 G>A), RS1000340102 (18:609696 T>C), RS1000445197 (18:644173 C>G,T), RS1000495655 (18:646040 A>G), RS1000553394 (18:641261 C>T), RS1000570484 (18:597177 C>A), RS1000594145 (18:599727 T>C), RS1000613219 (18:615327 G>T), RS1000616921 (18:638067 G>C)

Disease associations

OMIM: gene MIM:616990 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

2 associations (top):

Study	Trait	p-value
GCST002709_3	Electroencephalogram traits	6.000000e-06
GCST004635_37	Testicular germ cell tumor	4.000000e-10

EFO canonical traits (2, from GWAS)

EFO ID	Trait name
EFO:0004357	electroencephalogram measurement
EFO:0006870	alpha wave measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

15 total (human), top 15 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects expression, increases expression	4
mono-(2-ethylhexyl)phthalate	decreases expression	1
aflatoxin B2	decreases methylation	1
perfluorooctane sulfonic acid	affects expression	1
CGP 52608	affects binding, increases reaction	1
entinostat	increases expression	1
Resveratrol	affects cotreatment, decreases expression	1
Benzo(a)pyrene	increases methylation	1
Cadmium	decreases expression, increases abundance	1
Lead	affects expression	1
Plant Extracts	decreases expression, affects cotreatment	1
Cyclosporine	increases methylation	1
Aflatoxin B1	increases methylation	1
Cadmium Chloride	increases abundance, decreases expression	1
Okadaic Acid	decreases expression	1

Clinical trials (associated diseases)

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