UBQLNL

Summary

UBQLNL (ubiquilin like, HGNC:28294) is a protein-coding gene on chromosome 11p15.4, encoding Ubiquilin-like protein (Q8IYU4).

Predicted to enable polyubiquitin modification-dependent protein binding activity. Predicted to be involved in ubiquitin-dependent protein catabolic process. Predicted to be active in cytosol.

Source: NCBI Gene 143630 — RefSeq curated summary.

At a glance

• GWAS associations: 3
• Clinical variants (ClinVar): 76 total
• MANE Select transcript: NM_145053

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:28294
Approved symbol	UBQLNL
Name	ubiquilin like
Location	11p15.4
Locus type	gene with protein product
Status	Approved
Aliases	MGC20470, MGC26958
Ensembl gene	ENSG00000175518
Ensembl biotype	protein_coding
Entrez	143630

Gene structure

Transcript identifiers

Ensembl transcripts: 2 — 2 protein_coding

ENST00000380184, ENST00000673910

RefSeq mRNA: 1 — MANE Select: NM_145053 NM_145053

CCDS: CCDS31385

Canonical transcript exons

ENST00000380184 — 1 exons

Exon	Start	End
ENSE00001189637	5514393	5516699

Expression profiles

Bgee: expression breadth ubiquitous, 143 present calls, max score 95.36.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.0396 / max 32.9634, expressed in 3 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter ID	TPM avg	Samples expressed
118377	0.0254	3
118378	0.0058	3
118376	0.0056	3
118379	0.0028	2

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
sperm	CL:0000019	95.36	gold quality
left testis	UBERON:0004533	87.34	gold quality
right testis	UBERON:0004534	87.17	gold quality
testis	UBERON:0000473	84.43	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	80.99	gold quality
buccal mucosa cell	CL:0002336	68.70	gold quality
adult organism	UBERON:0007023	67.27	gold quality
left ovary	UBERON:0002119	64.07	gold quality
stromal cell of endometrium	CL:0002255	62.45	gold quality
right ovary	UBERON:0002118	62.39	gold quality
cauda epididymis	UBERON:0004360	59.89	gold quality
granulocyte	CL:0000094	59.87	gold quality
right uterine tube	UBERON:0001302	59.84	gold quality
mucosa of paranasal sinus	UBERON:0005030	59.52	gold quality
ovary	UBERON:0000992	59.35	gold quality
endocervix	UBERON:0000458	59.19	gold quality
parotid gland	UBERON:0001831	58.93	gold quality
body of uterus	UBERON:0009853	58.91	gold quality
spleen	UBERON:0002106	58.82	gold quality
lower esophagus mucosa	UBERON:0035834	58.74	gold quality
apex of heart	UBERON:0002098	58.65	gold quality
skeletal muscle tissue of biceps brachii	UBERON:0004502	58.63	gold quality
caput epididymis	UBERON:0004358	58.03	silver quality
right lobe of liver	UBERON:0001114	57.87	gold quality
ascending aorta	UBERON:0001496	57.70	gold quality
right adrenal gland	UBERON:0001233	57.51	gold quality
thoracic aorta	UBERON:0001515	57.51	gold quality
right lobe of thyroid gland	UBERON:0001119	57.18	gold quality
pigmented layer of retina	UBERON:0001782	57.15	gold quality
ectocervix	UBERON:0012249	57.01	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	2.43

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

40 targeting UBQLNL, 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-103A-3P	99.98	69.14	1595
HSA-MIR-107	99.98	69.14	1595
HSA-MIR-548AN	99.97	70.91	2817
HSA-MIR-497-5P	99.92	71.83	2674
HSA-MIR-15A-5P	99.90	72.80	2787
HSA-MIR-15B-5P	99.90	72.78	2798
HSA-MIR-16-5P	99.90	72.80	2780
HSA-MIR-195-5P	99.90	72.81	2805
HSA-MIR-424-5P	99.89	71.90	2641
HSA-MIR-6838-5P	99.89	71.94	2690
HSA-MIR-1976	99.74	65.48	1127
HSA-MIR-646	99.68	67.84	1645
HSA-MIR-10394-5P	99.65	66.83	1852
HSA-MIR-1205	99.65	66.76	1826
HSA-MIR-4524A-5P	99.57	71.73	1193
HSA-MIR-4524B-5P	99.57	71.68	1195
HSA-MIR-671-5P	99.52	67.11	1277
HSA-MIR-7151-5P	99.37	67.82	613
HSA-MIR-6828-5P	99.31	69.21	1433
HSA-MIR-18A-5P	99.29	71.05	806
HSA-MIR-18B-5P	99.29	71.05	806
HSA-MIR-4735-3P	99.14	69.85	777
HSA-MIR-3127-3P	98.94	67.34	1055
HSA-MIR-6756-3P	98.94	66.79	1104
HSA-MIR-876-3P	98.76	68.23	945
HSA-MIR-3908	98.75	67.31	1160
HSA-MIR-222-5P	98.75	69.17	1242
HSA-MIR-330-5P	98.73	67.63	1788
HSA-MIR-2467-3P	98.65	67.18	1969
HSA-MIR-1910-3P	98.44	67.51	1695

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
mus_musculus	Ubqlnl	ENSMUSG00000051437
rattus_norvegicus	Ubqlnl	ENSRNOG00000017016
drosophila_melanogaster	CG31528	FBGN0051528

Paralogs (5): UBQLN1 (ENSG00000135018), UBL7 (ENSG00000138629), UBQLN4 (ENSG00000160803), UBQLN3 (ENSG00000175520), UBQLN2 (ENSG00000188021)

Protein

Protein identifiers

Ubiquilin-like protein — Q8IYU4 (reviewed: Q8IYU4)

All UniProt accessions (2): Q8IYU4, A0A669KBE4

UniProt curated annotations — full annotation on UniProt →

Isoforms (2)

UniProt ID	Names	Canonical?
Q8IYU4-1	1	yes
Q8IYU4-2	2

RefSeq proteins (1): NP_659490* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR000626	Ubiquitin-like_dom	Domain
IPR015496	Ubiquilin	Family
IPR029071	Ubiquitin-like_domsf	Homologous_superfamily

Pfam: PF00240, PF23195

UniProt features (16 total): sequence variant 8, sequence conflict 2, region of interest 2, chain 1, domain 1, compositionally biased region 1, splice variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8IYU4-F1	55.37	0.12

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 46 (showing top): GOBP_MACROMOLECULE_CATABOLIC_PROCESS, GGGTGGRR_PAX4_03, YGACNNYACAR_UNKNOWN, TGANTCA_AP1_C, GOBP_PROTEIN_CATABOLIC_PROCESS, TGGAAA_NFAT_Q4_01, GOBP_PROTEOLYSIS, SREBP1_Q6, MARTENS_TRETINOIN_RESPONSE_UP, RP58_01, ZWANG_TRANSIENTLY_UP_BY_2ND_EGF_PULSE_ONLY, GOMF_POLYUBIQUITIN_MODIFICATION_DEPENDENT_PROTEIN_BINDING, GOMF_MODIFICATION_DEPENDENT_PROTEIN_BINDING, MIR15A_5P, MIR195_5P

GO Biological Process (1): ubiquitin-dependent protein catabolic process (GO:0006511)

GO Molecular Function (2): polyubiquitin modification-dependent protein binding (GO:0031593), protein binding (GO:0005515)

GO Cellular Component (1): cytosol (GO:0005829)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
protein ubiquitination	1
modification-dependent protein catabolic process	1
modification-dependent protein binding	1
binding	1
cytoplasm	1
cellular anatomical structure	1

Protein interactions and networks

STRING

2812 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
UBQLNL	OR52H1	Q8NGJ2	544
UBQLNL	STIP1	P31948	519
UBQLNL	PSMD4	P55036	468
UBQLNL	RALGPS2	Q86X27	467
UBQLNL	SPMIP10	Q6ZNM6	435
UBQLNL	HSPA4	P34932	373
UBQLNL	ADRM1	Q16186	363
UBQLNL	RAD23A	P54725	359
UBQLNL	BCL2L10	Q9HD36	357
UBQLNL	DESI2	Q9BSY9	353
UBQLNL	SPATA33	Q96N06	352
UBQLNL	IDNK	Q5T6J7	346
UBQLNL	ACTL7A	Q9Y615	344
UBQLNL	PSMD2	Q13200	338
UBQLNL	ESYT2	A0FGR8	326

IntAct

28 interactions, top by confidence:

A	B	Type	Score
DESI1	UBQLNL	psi-mi:“MI:0915”(physical association)	0.560
HGS	UBQLNL	psi-mi:“MI:0915”(physical association)	0.560
UBQLNL	ASPA	psi-mi:“MI:0915”(physical association)	0.560
HEXB	UBQLNL	psi-mi:“MI:0915”(physical association)	0.560
KLF11	UBQLNL	psi-mi:“MI:0915”(physical association)	0.560
UBQLNL	ATXN10	psi-mi:“MI:0915”(physical association)	0.560
UBQLNL	JPH3	psi-mi:“MI:0915”(physical association)	0.560
TARDBP	UBQLNL	psi-mi:“MI:0915”(physical association)	0.560
DESI1	UBQLNL	psi-mi:“MI:0915”(physical association)	0.000
HGS	UBQLNL	psi-mi:“MI:0915”(physical association)	0.000
UBQLNL	DESI1	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (5): UBQLNL (Two-hybrid), UBQLNL (Affinity Capture-MS), UBQLNL (Two-hybrid), HGS (Two-hybrid), UBQLNL (Two-hybrid)

ESM2 similar proteins: A7E371, A9RVK2, A9RZ57, F4I8S3, F4IEY4, F4IXN6, F4JTJ9, F4KFS7, O14097, O23215, O60291, O64571, O64763, O81472, P07249, P0C034, P0C2X8, P22575, P88825, Q09394, Q0P3R5, Q0WQ91, Q2QUS0, Q570X5, Q587J6, Q58FY4, Q5NVP2, Q5PP28, Q5XIQ4, Q5Z5Q3, Q5ZLK2, Q6K762, Q75JF2, Q794H2, Q7X9V2, Q7Z2Y5, Q8IYU4, Q8L8L9, Q8RXD3, Q8W4P8

Diamond homologs: Q14DL0, Q5R684, Q5XIP4, Q8IYU4, Q8R317, Q9UMX0, Q9H347, Q9JJP9, P49633, Q54L35, Q8C5U9, Q99NB8, Q9NRR5, Q9QZM0, Q9SII8, Q9SII9, Q9UHD9, Q9NIF3, A3KPW9, G5EFF7, P48510, Q10169, O42967, Q91W67

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	68
Likely benign	5
Benign	3

Top pathogenic / likely-pathogenic (0)

SpliceAI

140 predictions. Top by Δscore:

Variant	Effect	Δscore
11:5515161:T:TA	donor_gain	0.8900
11:5518308:A:AC	donor_gain	0.8900
11:5518309:C:CC	donor_gain	0.8900
11:5515101:TGTGA:T	donor_gain	0.8800
11:5515088:G:C	donor_gain	0.8500
11:5515249:T:TA	donor_gain	0.8500
11:5515234:A:AC	donor_gain	0.8100
11:5518392:TTC:T	donor_gain	0.7700
11:5518393:TCT:T	donor_gain	0.7700
11:5515203:A:AC	donor_gain	0.7600
11:5514925:A:AT	donor_gain	0.7400
11:5514488:ATT:A	donor_gain	0.7300
11:5515429:C:CT	donor_gain	0.7300
11:5515235:G:C	donor_gain	0.7200
11:5518326:T:TA	donor_gain	0.6900
11:5515158:G:A	donor_gain	0.6700
11:5514847:ATTC:A	acceptor_gain	0.6500
11:5514848:TTCC:T	acceptor_gain	0.6400
11:5515699:A:C	donor_gain	0.6300
11:5515698:A:AC	donor_gain	0.6200
11:5515430:C:CT	donor_gain	0.6100
11:5518049:A:AC	donor_gain	0.6000
11:5518050:C:CC	donor_gain	0.6000
11:5518303:A:AT	donor_gain	0.6000
11:5515025:G:C	donor_gain	0.5900
11:5515189:T:C	donor_gain	0.5900
11:5518310:T:C	donor_gain	0.5700
11:5518309:CT:C	donor_gain	0.5600
11:5515098:A:AC	donor_gain	0.5400
11:5515099:C:CC	donor_gain	0.5400

AlphaMissense

3162 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
11:5516220:G:C	F74L	0.943
11:5516220:G:T	F74L	0.943
11:5516222:A:G	F74L	0.943
11:5516274:C:A	K56N	0.909
11:5516274:C:G	K56N	0.909
11:5516310:A:C	F44L	0.875
11:5516310:A:T	F44L	0.875
11:5516312:A:G	F44L	0.875
11:5516173:A:G	I90T	0.823
11:5516253:G:C	F63L	0.821
11:5516253:G:T	F63L	0.821
11:5516255:A:G	F63L	0.821
11:5516338:A:T	V35E	0.804
11:5516173:A:C	I90S	0.774
11:5516155:A:T	I96N	0.766
11:5516278:A:G	F55S	0.766
11:5516155:A:C	I96S	0.754
11:5516311:A:G	F44S	0.742
11:5516146:A:T	V99D	0.738
11:5516206:A:T	L79H	0.726
11:5516155:A:G	I96T	0.717
11:5516224:A:T	V73D	0.703
11:5516139:C:A	K101N	0.696
11:5516139:C:G	K101N	0.696
11:5516277:G:C	F55L	0.696
11:5516277:G:T	F55L	0.696
11:5516279:A:G	F55L	0.696
11:5516334:C:A	K36N	0.689
11:5516334:C:G	K36N	0.689
11:5516344:A:T	V33E	0.682

dbSNP variants (sampled 300 via entrez): RS1001052588 (11:5516961 G>A), RS1001086988 (11:5516746 C>G,T), RS1001569880 (11:5516289 C>T), RS1001691107 (11:5517271 C>CT), RS1001995049 (11:5517640 C>A,G,T), RS1002579368 (11:5517581 G>A,C), RS1004334488 (11:5518536 C>A,G,T), RS1004346123 (11:5515383 G>C,T), RS1004951518 (11:5516581 G>T), RS1005384206 (11:5516315 C>A), RS1006365969 (11:5517886 T>C), RS1006546686 (11:5516191 G>A,T), RS1007412663 (11:5518284 A>T), RS1008288306 (11:5513937 T>C), RS1010086694 (11:5516341 A>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

3 associations (top):

Study	Trait	p-value
GCST010725_20	Malaria	4.000000e-69
GCST010725_33	Malaria	2.000000e-67
GCST010725_51	Malaria	1.000000e-55

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
Benzo(a)pyrene	increases mutagenesis, decreases expression, increases methylation	3
sodium arsenite	decreases expression	2
propionaldehyde	increases expression	1
butyraldehyde	decreases expression	1
S-(1,2-dichlorovinyl)cysteine	affects response to substance, increases expression	1
di-n-butylphosphoric acid	affects expression	1
Sunitinib	increases expression	1
Leflunomide	decreases expression	1
Arsenic	affects methylation	1
Diethylhexyl Phthalate	decreases expression	1
Lipopolysaccharides	affects response to substance, increases expression	1
Silicon Dioxide	affects expression	1
Tetrachlorodibenzodioxin	affects expression	1
Tretinoin	increases expression	1
Valproic Acid	decreases expression	1
Aflatoxin B1	increases methylation	1
Cadmium Chloride	decreases expression	1

Clinical trials (associated diseases)

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