USP17L13

Summary

USP17L13 (ubiquitin specific peptidase 17 like family member 13, HGNC:44441) is a protein-coding gene on chromosome 4p16.1, encoding Ubiquitin carboxyl-terminal hydrolase 17-like protein 13 (C9JLJ4). Deubiquitinating enzyme that removes conjugated ubiquitin from specific proteins to regulate different cellular processes that may include cell proliferation, progression through the cell cycle, apoptosis, cell migration, and the cellular response to viral infection.

Predicted to enable cysteine-type deubiquitinase activity. Predicted to be involved in regulation of apoptotic process and regulation of protein stability. Predicted to be located in endoplasmic reticulum. Predicted to be active in cytosol and nucleus.

Source: NCBI Gene 100287238 — RefSeq curated summary.

At a glance

• MANE Select transcript: NM_001256855

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:44441
Approved symbol	USP17L13
Name	ubiquitin specific peptidase 17 like family member 13
Location	4p16.1
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000232399
Ensembl biotype	protein_coding
Entrez	100287238

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000429667

RefSeq mRNA: 1 — MANE Select: NM_001256855 NM_001256855

CCDS: CCDS59457

Canonical transcript exons

ENST00000429667 — 1 exons

Exon	Start	End
ENSE00001674189	9224896	9226488

Expression profiles

Bgee: expression breadth not_expressed, 0 present calls, max score 39.87.

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
cortical plate	UBERON:0005343	39.87	gold quality
colonic epithelium	UBERON:0000397	37.20	gold quality
ventricular zone	UBERON:0003053	36.48	gold quality
bone marrow cell	CL:0002092	36.16	gold quality
ganglionic eminence	UBERON:0004023	35.49	gold quality
skeletal muscle tissue	UBERON:0001134	34.79	gold quality
muscle tissue	UBERON:0002385	33.17	gold quality
bone marrow	UBERON:0002371	32.79	gold quality
hindlimb stylopod muscle	UBERON:0004252	32.15	gold quality
sural nerve	UBERON:0015488	30.93	gold quality
superior frontal gyrus	UBERON:0002661	30.58	gold quality
stromal cell of endometrium	CL:0002255	29.87	gold quality
prefrontal cortex	UBERON:0000451	29.04	gold quality
lymph node	UBERON:0000029	28.67	gold quality
duodenum	UBERON:0002114	28.14	gold quality
liver	UBERON:0002107	28.04	gold quality
smooth muscle tissue	UBERON:0001135	27.28	gold quality
tonsil	UBERON:0002372	27.05	gold quality
islet of Langerhans	UBERON:0000006	26.88	gold quality
vermiform appendix	UBERON:0001154	26.42	gold quality
blood	UBERON:0000178	26.33	gold quality
gall bladder	UBERON:0002110	25.98	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	25.89	gold quality
placenta	UBERON:0001987	25.81	gold quality
urinary bladder	UBERON:0001255	25.72	gold quality
muscle of leg	UBERON:0001383	25.33	gold quality
leukocyte	CL:0000738	24.80	gold quality
calcaneal tendon	UBERON:0003701	24.73	gold quality
primary visual cortex	UBERON:0002436	24.61	gold quality
kidney	UBERON:0002113	24.53	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	0.00

Regulation

Is transcription factor: no

Cross-species orthologs

0 orthologs

Paralogs (71): USP2 (ENSG00000036672), USP28 (ENSG00000048028), USP36 (ENSG00000055483), USP13 (ENSG00000058056), USP33 (ENSG00000077254), USP40 (ENSG00000085982), USP48 (ENSG00000090686), USP14 (ENSG00000101557), USP11 (ENSG00000102226), USP10 (ENSG00000103194), USP31 (ENSG00000103404), USP42 (ENSG00000106346), USP5 (ENSG00000111667), USP4 (ENSG00000114316), USP9Y (ENSG00000114374), USP34 (ENSG00000115464), USP35 (ENSG00000118369), USP45 (ENSG00000123552), USP22 (ENSG00000124422), USP9X (ENSG00000124486), USP6 (ENSG00000129204), USP29 (ENSG00000131864), USP26 (ENSG00000134588), USP30 (ENSG00000135093), USP15 (ENSG00000135655), USP37 (ENSG00000135913), USP44 (ENSG00000136014), USP20 (ENSG00000136878), USP8 (ENSG00000138592), USP3 (ENSG00000140455), USP21 (ENSG00000143258), USP43 (ENSG00000154914), USP25 (ENSG00000155313), USP16 (ENSG00000156256), USP24 (ENSG00000162402), USP1 (ENSG00000162607), USP49 (ENSG00000164663), USP38 (ENSG00000170185), USP50 (ENSG00000170236), USP47 (ENSG00000170242)

Protein

Protein identifiers

Ubiquitin carboxyl-terminal hydrolase 17-like protein 13 — C9JLJ4 (reviewed: C9JLJ4)

All UniProt accessions (1): C9JLJ4

UniProt curated annotations — full annotation on UniProt →

Function. Deubiquitinating enzyme that removes conjugated ubiquitin from specific proteins to regulate different cellular processes that may include cell proliferation, progression through the cell cycle, apoptosis, cell migration, and the cellular response to viral infection.

Subcellular location. Nucleus. Endoplasmic reticulum.

Similarity. Belongs to the peptidase C19 family. USP17 subfamily.

RefSeq proteins (1): NP_001243784* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001394	Peptidase_C19_UCH	Domain
IPR018200	USP_CS	Conserved_site
IPR028889	USP	Domain
IPR038765	Papain-like_cys_pep_sf	Homologous_superfamily
IPR050164	Peptidase_C19	Family

Pfam: PF00443

UniProt features (10 total): compositionally biased region 4, region of interest 2, active site 2, chain 1, domain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-C9JLJ4-F1	68.26	0.45

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): 89 (nucleophile); 334 (proton acceptor)

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

ID	Pathway
R-HSA-5689880	Ub-specific processing proteases

MSigDB gene sets: 14 (showing top): GOBP_PROTEIN_MODIFICATION_BY_SMALL_PROTEIN_REMOVAL, GOMF_CYSTEINE_TYPE_PEPTIDASE_ACTIVITY, chr4p16, GOBP_POST_TRANSLATIONAL_PROTEIN_MODIFICATION, GOBP_REGULATION_OF_PROTEIN_STABILITY, GOBP_PROTEOLYSIS, GOMF_PEPTIDASE_ACTIVITY, GOMF_UBIQUITIN_LIKE_PROTEIN_PEPTIDASE_ACTIVITY, REACTOME_POST_TRANSLATIONAL_PROTEIN_MODIFICATION, REACTOME_DEUBIQUITINATION, REACTOME_UB_SPECIFIC_PROCESSING_PROTEASES, GOBP_REGULATION_OF_PROGRAMMED_CELL_DEATH, GOBP_PROTEIN_MODIFICATION_PROCESS, GOMF_DEUBIQUITINASE_ACTIVITY

GO Biological Process (4): proteolysis (GO:0006508), protein deubiquitination (GO:0016579), regulation of protein stability (GO:0031647), regulation of apoptotic process (GO:0042981)

GO Molecular Function (4): cysteine-type deubiquitinase activity (GO:0004843), peptidase activity (GO:0008233), cysteine-type peptidase activity (GO:0008234), hydrolase activity (GO:0016787)

GO Cellular Component (3): nucleus (GO:0005634), endoplasmic reticulum (GO:0005783), cytosol (GO:0005829)

Reactome top-level categories

Rollup of top-1 pathways:

Category	Pathways
Deubiquitination	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
intracellular membrane-bounded organelle	2
cytoplasm	2
protein metabolic process	1
cysteine-type deubiquitinase activity	1
protein modification by small protein removal	1
regulation of biological quality	1
apoptotic process	1
regulation of programmed cell death	1
cysteine-type peptidase activity	1
deubiquitinase activity	1
hydrolase activity	1
catalytic activity, acting on a protein	1
peptidase activity	1
catalytic activity	1
endomembrane system	1
cellular anatomical structure	1

Protein interactions and networks

STRING

86 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
USP17L13	RGPD4	Q7Z3J3	570
USP17L13	ANKRD36	A6QL64	447
USP17L13	AP4B1	Q9Y6B7	411
USP17L13	RRP1B	Q14684	395
USP17L13	PCBD1	P61457	352
USP17L13	POLR1A	O95602	349
USP17L13	CDC27	P30260	247
USP17L13	RANBP2	P49792	240
USP17L13	PPP1R3A	Q16821	231
USP17L13	PCNT	O95613	222
USP17L13	TNFRSF11A	Q9Y6Q6	216
USP17L13	CFAP251	Q8TBY9	211
USP17L13	TNFRSF11B	O00300	202
USP17L13	ATPAF1	Q5TC12	197
USP17L13	MUC5B	Q9HC84	196

IntAct

2 interactions, top by confidence:

A	B	Type	Score
M		psi-mi:“MI:0914”(association)	0.350

BioGRID (3): USP17L13 (Affinity Capture-MS), USP17L13 (Affinity Capture-MS), USP17L13 (Affinity Capture-MS)

ESM2 similar proteins: A2A5N8, A6NCW0, A6NCW7, A8MUK1, B1AQJ2, B2RQC2, C9J2P7, C9JJH3, C9JLJ4, C9JPN9, C9JVI0, D3ZWK4, D6R901, D6R9N7, D6RA61, D6RBM5, D6RBQ6, D6RCP7, D6RJB6, E9Q9U0, G5E8G2, G5E8I7, O94966, P0C7H9, P0C7I0, P35125, P51784, Q0E2F9, Q0WX57, Q2TAC6, Q3UJD6, Q4KLL9, Q5R7G8, Q5TKR9, Q61068, Q66HE5, Q6J1Y9, Q6PFD6, Q6QN14, Q6R6M4

Diamond homologs: A1L1K8, A6NCW0, A6NCW7, A8MUK1, C9J2P7, C9JJH3, C9JLJ4, C9JPN9, C9JVI0, D6R901, D6R9N7, D6RA61, D6RBQ6, D6RCP7, D6RJB6, G1SW77, P0C7H9, P0C7I0, Q0WX57, Q5JVS0, Q5XJA5, Q6AXS5, Q6NRY1, Q6PB22, Q6R6M4, Q7RTZ2, Q8NC51, Q9CY58, Q9I9R0, Q9JKS5, A0JM59, A5PMR2, A5PN09, A6H8I0, A6NNY8, A6QNM7, A7Z056, B1AY13, B1WBD7, D3ZJ96

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

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

Top pathogenic / likely-pathogenic (0)

SpliceAI

69 predictions. Top by Δscore:

Variant	Effect	Δscore
4:9226186:G:GT	donor_gain	0.6000
4:9226187:A:T	donor_gain	0.5700
4:9226169:TGGA:T	donor_gain	0.5000
4:9226260:CGAAG:C	donor_loss	0.4700
4:9226261:GAAGG:G	donor_loss	0.4700
4:9226262:AAGGT:A	donor_loss	0.4700
4:9226263:AGG:A	donor_loss	0.4700
4:9226264:GG:G	donor_loss	0.4700
4:9226265:G:C	donor_loss	0.4700
4:9226266:T:G	donor_loss	0.4700
4:9225994:GCC:G	donor_gain	0.4500
4:9226259:TCGAA:T	donor_loss	0.4300
4:9225071:C:T	donor_gain	0.4200
4:9226259:TCGA:T	donor_gain	0.4200
4:9226267:A:C	donor_loss	0.4200
4:9226113:A:T	donor_gain	0.4000
4:9225877:TG:T	donor_gain	0.3800
4:9225878:GG:G	donor_gain	0.3800
4:9226099:C:T	donor_gain	0.3800
4:9226013:T:G	acceptor_gain	0.3600
4:9226233:G:GT	donor_gain	0.3600
4:9225103:C:G	donor_gain	0.3500
4:9226039:A:AG	donor_gain	0.3300
4:9226040:G:GG	donor_gain	0.3300
4:9225033:G:GT	donor_gain	0.3200
4:9225090:G:GT	donor_gain	0.3200
4:9225103:C:CG	donor_gain	0.3200
4:9226170:GGAA:G	donor_gain	0.3100
4:9226236:GCC:G	donor_gain	0.3100
4:9225833:G:GT	donor_gain	0.3000

AlphaMissense

3493 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
4:9225742:T:C	F283L	0.998
4:9225744:C:A	F283L	0.998
4:9225744:C:G	F283L	0.998
4:9225947:A:T	D351V	0.997
4:9225948:T:A	D351E	0.997
4:9225948:T:G	D351E	0.997
4:9225931:T:A	W346R	0.994
4:9225931:T:C	W346R	0.994
4:9225946:G:C	D351H	0.994
4:9225947:A:C	D351A	0.994
4:9225147:T:A	N84K	0.993
4:9225147:T:G	N84K	0.993
4:9225375:T:A	D160E	0.993
4:9225375:T:G	D160E	0.993
4:9225893:G:A	G333E	0.993
4:9225385:T:C	F164L	0.992
4:9225387:T:A	F164L	0.992
4:9225387:T:G	F164L	0.992
4:9225897:T:A	H334Q	0.992
4:9225897:T:G	H334Q	0.992
4:9225893:G:T	G333V	0.991
4:9225683:C:A	A263D	0.990
4:9225690:G:C	K265N	0.990
4:9225690:G:T	K265N	0.990
4:9225947:A:G	D351G	0.990
4:9225593:T:A	V233D	0.989
4:9225734:T:C	L280S	0.989
4:9225895:C:G	H334D	0.989
4:9225352:T:C	F153L	0.988
4:9225354:C:A	F153L	0.988

dbSNP variants (sampled 300 via entrez): RS1030915230 (4:9223625 G>C), RS1158547769 (4:9224085 T>G), RS1159195425 (4:9225934 T>G), RS1162180987 (4:9225899 A>C,G), RS1163103824 (4:9224080 T>G), RS1163860679 (4:9226355 T>A), RS1165712788 (4:9223909 T>G), RS1168018310 (4:9223768 A>G), RS1168250731 (4:9224193 T>A), RS1170253797 (4:9226334 C>A), RS1170551017 (4:9226206 G>A), RS1171943251 (4:9224401 A>C), RS1172357310 (4:9223902 A>G), RS1172564614 (4:9223611 C>A,T), RS1174475285 (4:9224218 G>T)

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

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

1 total (human), top 1 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
2-palmitoylglycerol	increases expression	1

Clinical trials (associated diseases)

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