UBE2NL

Summary

UBE2NL (ubiquitin conjugating enzyme E2 N like (gene/pseudogene), HGNC:31710) is a protein-coding gene on chromosome Xq27.3, encoding Putative ubiquitin-conjugating enzyme E2 N-like (Q5JXB2).

This gene is intronless and encodes a member of the ubiquitin-conjugating enzyme family. The protein product is 91% identical to ubiquitin-conjugating enzyme E2N, a multi-exon gene product. This locus represents a polymorphic pseudogene, where some individuals contain an allele that can encode a full-length protein, while others have a non-functional allele containing a premature stop codon (reference SNP rs237520) that truncates the coding sequence.

Source: NCBI Gene 389898 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 22 total

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:31710
Approved symbol	UBE2NL
Name	ubiquitin conjugating enzyme E2 N like (gene/pseudogene)
Location	Xq27.3
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000276380
Ensembl biotype	protein_coding
Entrez	389898

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding_LoF

ENST00000618570

RefSeq mRNA: 0 — MANE Select: None

Canonical transcript exons

ENST00000618570 — 1 exons

Exon	Start	End
ENSE00003740347	143884071	143885255

Expression profiles

Bgee: expression breadth ubiquitous, 170 present calls, max score 97.13.

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
gingival epithelium	UBERON:0001949	97.13	silver quality
gingiva	UBERON:0001828	96.05	silver quality
adult organism	UBERON:0007023	94.71	silver quality
superficial temporal artery	UBERON:0001614	94.64	silver quality
hair follicle	UBERON:0002073	94.62	silver quality
heart right ventricle	UBERON:0002080	94.58	silver quality
mucosa of sigmoid colon	UBERON:0004993	94.58	silver quality
oral cavity	UBERON:0000167	94.13	silver quality
myocardium	UBERON:0002349	93.89	silver quality
mammalian vulva	UBERON:0000997	93.72	silver quality
diaphragm	UBERON:0001103	93.56	silver quality
left ventricle myocardium	UBERON:0006566	93.48	silver quality
cervix squamous epithelium	UBERON:0006922	93.36	silver quality
skeletal muscle tissue of biceps brachii	UBERON:0004502	93.20	silver quality
cervix epithelium	UBERON:0004801	93.14	silver quality
vastus lateralis	UBERON:0001379	92.99	silver quality
skeletal muscle tissue of rectus abdominis	UBERON:0004511	92.94	silver quality
biceps brachii	UBERON:0001507	92.66	silver quality
cardiac muscle of right atrium	UBERON:0003379	92.55	silver quality
vena cava	UBERON:0004087	92.51	silver quality
orbitofrontal cortex	UBERON:0004167	92.49	silver quality
colonic mucosa	UBERON:0000317	92.47	silver quality
quadriceps femoris	UBERON:0001377	92.41	silver quality
cardia of stomach	UBERON:0001162	92.30	silver quality
nasal cavity epithelium	UBERON:0005384	92.26	silver quality
Brodmann (1909) area 46	UBERON:0006483	92.02	silver quality
cauda epididymis	UBERON:0004360	91.84	gold quality
germinal epithelium of ovary	UBERON:0001304	91.79	silver quality
male germ cell	CL:0000015	91.57	silver quality
mucosa of paranasal sinus	UBERON:0005030	91.57	silver quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	8.03
E-MTAB-3929	yes	4.56

Regulation

Is transcription factor: no

Cross-species orthologs

6 orthologs

Organism	Symbol	Gene ID
danio_rerio	ube2na	ENSDARG00000008748
danio_rerio	ube2nb	ENSDARG00000045877
rattus_norvegicus		ENSRNOG00000063895
drosophila_melanogaster	ben	FBGN0000173
drosophila_melanogaster	CG3473	FBGN0028913
caenorhabditis_elegans		WBGENE00006708

Paralogs (24): UBE2T (ENSG00000077152), UBE2A (ENSG00000077721), UBE2K (ENSG00000078140), CDC34 (ENSG00000099804), UBE2I (ENSG00000103275), UBE2W (ENSG00000104343), UBE2R2 (ENSG00000107341), UBE2S (ENSG00000108106), UBE2B (ENSG00000119048), UBE2G1 (ENSG00000132388), UBE2Z (ENSG00000159202), UBE2J2 (ENSG00000160087), AKTIP (ENSG00000166971), UBE2V2 (ENSG00000169139), UBE2C (ENSG00000175063), UBE2O (ENSG00000175931), UBE2U (ENSG00000177414), UBE2N (ENSG00000177889), UBE2F (ENSG00000184182), UBE2G2 (ENSG00000184787), UBE2H (ENSG00000186591), UBE2J1 (ENSG00000198833), PEDS1 (ENSG00000240849), UBE2V1 (ENSG00000244687)

Protein

Protein identifiers

Putative ubiquitin-conjugating enzyme E2 N-like — Q5JXB2 (reviewed: Q5JXB2)

Alternative names: Epididymis tissue protein Li 174

All UniProt accessions (0):

UniProt curated annotations — full annotation on UniProt →

Tissue specificity. Expressed in epididymis (at protein level).

Similarity. Belongs to the ubiquitin-conjugating enzyme family.

RefSeq proteins (0): (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR000608	UBC	Domain
IPR016135	UBQ-conjugating_enzyme/RWD	Homologous_superfamily
IPR050113	Ub_conjugating_enzyme-E2-like	Family

Pfam: PF00179

Enzyme classification (BRENDA):

• EC 2.3.2.23 — E2 ubiquitin-conjugating enzyme (BRENDA: 20 organisms, 93 substrates, 28 inhibitors, 12 Km, 8 kcat entries)

Substrate kinetics (BRENDA)

4 substrates with measured Km, best-characterized 4. Km ranges are aggregated across organisms/conditions.

Substrate	Km (mM)	Measurements
[UBIQUITIN-CARRIER-PROTEIN UBC2B]-L-CYSTEINE	0.0001	5
[UBE2W]-S-UBIQUITINYL-L-CYSTEINE	0.2203–0.3014	2
S-UBIQUITINYL-[E1 UBIQUITIN-ACTIVATING ENZYME]-L	1	1
[UBIQUITIN CARRIER PROTEIN UBC4]-L-CYSTEINE	0.0019	1

UniProt features (3 total): chain 1, domain 1, modified residue 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q5JXB2-F1	92.02	0.79

Functional residue map

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

Post-translational modifications (1): 83

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 46 (showing top): GSE45365_CD8A_DC_VS_CD11B_DC_IFNAR_KO_MCMV_INFECTION_DN, GOBP_DNA_DAMAGE_TOLERANCE, AGTCTTA_MIR499, GOBP_DNA_DAMAGE_RESPONSE, GOBP_POST_TRANSLATIONAL_PROTEIN_MODIFICATION, GOBP_PROTEIN_POLYUBIQUITINATION, GOBP_PROTEIN_K63_LINKED_UBIQUITINATION, KEGG_UBIQUITIN_MEDIATED_PROTEOLYSIS, GTGACTT_MIR224, GOBP_DNA_REPLICATION, NAKAMURA_TUMOR_ZONE_PERIPHERAL_VS_CENTRAL_UP, GOBP_DNA_METABOLIC_PROCESS, GOMF_UBIQUITIN_LIKE_PROTEIN_CONJUGATING_ENZYME_ACTIVITY, GOMF_ACYLTRANSFERASE_ACTIVITY, GOMF_AMINOACYLTRANSFERASE_ACTIVITY

GO Biological Process (1): protein polyubiquitination (GO:0000209)

GO Molecular Function (1): ubiquitin conjugating enzyme activity (GO:0061631)

GO Cellular Component (2): nucleus (GO:0005634), extracellular exosome (GO:0070062)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
protein ubiquitination	1
ubiquitin-protein transferase activity	1
ubiquitin-like protein conjugating enzyme activity	1
intracellular membrane-bounded organelle	1
extracellular vesicle	1

Protein interactions and networks

STRING

0 interactions, top by confidence (×1000):

IntAct

7 interactions, top by confidence:

A	B	Type	Score
DUX4	CBX3	psi-mi:“MI:0914”(association)	0.350
CAV1	PPM1G	psi-mi:“MI:0914”(association)	0.350
CAV1	ACOT7	psi-mi:“MI:0914”(association)	0.350
VCAM1		psi-mi:“MI:0914”(association)	0.350

BioGRID (17): UBE2NL (Co-fractionation), UBE2NL (Affinity Capture-MS), UBE2NL (Affinity Capture-MS), UBE2NL (Affinity Capture-MS), UBE2NL (Affinity Capture-MS), UBE2NL (Affinity Capture-MS), UBE2NL (Proximity Label-MS), UBE2NL (Affinity Capture-MS), UBE2NL (Affinity Capture-MS), UBE2NL (Affinity Capture-MS), RPS27A (Cross-Linking-MS (XL-MS)), UBE2N (Cross-Linking-MS (XL-MS)), UBA52 (Cross-Linking-MS (XL-MS)), UBE2NL (Cross-Linking-MS (XL-MS)), UBE2NL (Affinity Capture-MS)

ESM2 similar proteins: I1RRW0, O00102, O74810, P0CS16, P0CS17, P21734, P25868, P35128, P40984, P52486, P52491, P56616, P61085, P61086, P61087, P61088, P61089, P62253, P62254, P62255, Q02159, Q0P5K3, Q1RMW1, Q28CQ4, Q32LD2, Q32PA5, Q3UWQ3, Q42540, Q4PFA5, Q4R4I1, Q4R5Y8, Q5JXB2, Q5M8Y2, Q5R7J6, Q5U203, Q5ZKX6, Q6IRC7, Q6NY82, Q6Y1Z4, Q75AF2

Diamond homologs: A1L3K1, A5PKP9, A7SE05, B5DFI8, C1C3R6, D3ZDK2, O13685, O74196, O74810, P0CS16, P0CS17, P15731, P15732, P21734, P25153, P25866, P25867, P35128, P35129, P35130, P35131, P35132, P35133, P35134, P35135, P42745, P42746, P43102, P46595, P49459, P51668, P51965, P52478, P52482, P52483, P52485, P52490, P61077, P61078, P61079

SIGNOR signaling

2 interactions.

A	Effect	B	Mechanism
“Ub:E1 (UBA1 substrate)”	“up-regulates activity”	UBE2NL	ubiquitination
“Ub:E1 (UBA6 substrate)”	“up-regulates activity”	UBE2NL	ubiquitination

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	18
Likely benign	3
Benign	1

Top pathogenic / likely-pathogenic (0)

SpliceAI

155 predictions. Top by Δscore:

Variant	Effect	Δscore
X:143884131:G:GT	donor_gain	0.6500
X:143884248:G:GT	donor_gain	0.6500
X:143884249:G:T	donor_gain	0.6500
X:143884249:G:GT	donor_gain	0.6000
X:143884839:GTT:G	donor_gain	0.5900
X:143884840:TTT:T	donor_gain	0.5900
X:143884186:A:T	donor_gain	0.5800
X:143884211:G:GA	donor_gain	0.5700
X:143884096:TTCTG:T	donor_gain	0.5600
X:143884183:A:G	donor_gain	0.5500
X:143884308:G:GG	donor_gain	0.5500
X:143884132:A:T	donor_gain	0.5400
X:143884233:G:GT	donor_gain	0.5400
X:143884803:G:GA	donor_gain	0.5200
X:143884889:GGGT:G	donor_gain	0.5000
X:143884890:GGTG:G	donor_gain	0.5000
X:143884845:G:GG	donor_gain	0.4900
X:143884838:GGTT:G	donor_gain	0.4800
X:143884844:A:AG	donor_gain	0.4800
X:143884871:T:G	donor_gain	0.4700
X:143884791:TTTAA:T	donor_gain	0.4600
X:143884841:T:G	donor_gain	0.4600
X:143884522:C:G	donor_gain	0.4400
X:143884880:T:A	donor_gain	0.4400
X:143884919:GGGGG:G	donor_gain	0.4400
X:143884920:GGGGG:G	donor_gain	0.4400
X:143884210:T:TA	donor_gain	0.4300
X:143884214:C:A	donor_gain	0.4300
X:143884786:AAAC:A	donor_gain	0.4300
X:143884841:TTA:T	donor_gain	0.4200

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1005018039 (X:143885740 A>C), RS1005612856 (X:143882729 A>G), RS1006123539 (X:143883073 A>G), RS1007067639 (X:143882236 A>G), RS1012914072 (X:143882776 T>G), RS1013010235 (X:143883125 T>C), RS1015996451 (X:143885749 G>T), RS1016315971 (X:143885292 A>T), RS1016908615 (X:143882369 A>G), RS1017418513 (X:143882750 T>G), RS1017458341 (X:143883939 C>T), RS1024278158 (X:143883141 A>T), RS1024351627 (X:143882824 T>C), RS1026265921 (X:143882341 G>C), RS1030026583 (X:143883695 C>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

1 associations (top):

Study	Trait	p-value
GCST009391_586	Metabolite levels	4.000000e-06

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0010501	indole-3-propionate measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

14 total (human), top 14 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
bisphenol A	decreases expression, affects cotreatment	2
K 7174	decreases expression	1
Acetaminophen	decreases expression	1
Air Pollutants	decreases expression, increases abundance	1
Atrazine	increases expression	1
Benztropine	increases expression	1
Dexamethasone	affects cotreatment, decreases expression	1
Haloperidol	increases expression	1
Indomethacin	affects cotreatment, decreases expression	1
Urethane	decreases expression	1
Valproic Acid	affects expression	1
1-Methyl-3-isobutylxanthine	affects cotreatment, decreases expression	1
Lactic Acid	decreases expression	1
Particulate Matter	decreases expression, increases abundance	1

Clinical trials (associated diseases)

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