RNF38

gene
On this page

Summary

RNF38 (ring finger protein 38, HGNC:18052) is a protein-coding gene on chromosome 9p13.2, encoding E3 ubiquitin-protein ligase RNF38 (Q9H0F5). Acts as an E3 ubiquitin-protein ligase able to ubiquitinate p53/TP53 which promotes its relocalization to discrete foci associated with PML nuclear bodies.

This gene encodes a protein with a coiled-coil motif and a RING-H2 motif (C3H2C2) at its carboxy-terminus. The RING motif is a zinc-binding domain found in a large set of proteins playing roles in diverse cellular processes including oncogenesis, development, signal transduction, and apoptosis. Multiple transcript variants encoding different isoforms have been found for this gene.

Source: NCBI Gene 152006 — RefSeq curated summary.

At a glance

  • GWAS associations: 1
  • Clinical variants (ClinVar): 82 total
  • MANE Select transcript: NM_022781

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:18052
Approved symbolRNF38
Namering finger protein 38
Location9p13.2
Locus typegene with protein product
StatusApproved
Ensembl geneENSG00000137075
Ensembl biotypeprotein_coding
OMIM612488
Entrez152006

Gene structure

Transcript identifiers

Ensembl transcripts: 10 — 7 protein_coding, 3 protein_coding_CDS_not_defined

ENST00000259605, ENST00000350199, ENST00000353739, ENST00000357058, ENST00000377877, ENST00000377885, ENST00000484621, ENST00000488058, ENST00000491349, ENST00000611646

RefSeq mRNA: 5 — MANE Select: NM_022781 NM_022781, NM_194328, NM_194329, NM_194330, NM_194332

CCDS: CCDS6603, CCDS6604

Canonical transcript exons

ENST00000259605 — 12 exons

ExonStartEnd
ENSE000006999213635111536351199
ENSE000007000133635317036353331
ENSE000007000803635630336356473
ENSE000008330963635274236352848
ENSE000012881833634483236344953
ENSE000016947633634232536342424
ENSE000019060813640009736400269
ENSE000035294723636971936369932
ENSE000035971813639046736390616
ENSE000036126703635777536357942
ENSE000036715763637593436376127
ENSE000038431533633640036339814

Expression profiles

Bgee: expression breadth ubiquitous, 292 present calls, max score 99.85.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 20.9550 / max 315.9184, expressed in 1803 samples.

FANTOM5 promoters (13 alternative TSS)

Promoter IDTPM avgSamples expressed
10069512.87101787
1006912.30131157
1006921.8095864
1006930.8037439
1006890.7151249
1006900.7018418
1006860.3717182
1006840.3467165
1006880.288399
1006850.2765135

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
spermCL:000001999.85gold quality
secondary oocyteCL:000065599.68gold quality
oocyteCL:000002398.63gold quality
male germ cellCL:000001597.99gold quality
left testisUBERON:000453396.53gold quality
right testisUBERON:000453496.42gold quality
cortical plateUBERON:000534395.80gold quality
ganglionic eminenceUBERON:000402395.59gold quality
testisUBERON:000047395.48gold quality
cauda epididymisUBERON:000436094.68gold quality
metanephric glomerulusUBERON:000473694.63gold quality
germinal epithelium of ovaryUBERON:000130494.59gold quality
choroid plexus epitheliumUBERON:000391194.51gold quality
adult organismUBERON:000702394.44gold quality
renal glomerulusUBERON:000007494.42gold quality
Brodmann (1909) area 23UBERON:001355494.10gold quality
corpus epididymisUBERON:000435994.03gold quality
parietal pleuraUBERON:000240093.44gold quality
endothelial cellCL:000011593.34gold quality
embryoUBERON:000092293.30gold quality
middle temporal gyrusUBERON:000277193.27gold quality
trabecular bone tissueUBERON:000248393.06gold quality
esophagus squamous epitheliumUBERON:000692093.01gold quality
visceral pleuraUBERON:000240192.95gold quality
superficial temporal arteryUBERON:000161492.80gold quality
pleuraUBERON:000097792.72gold quality
caput epididymisUBERON:000435892.67gold quality
seminal vesicleUBERON:000099892.22gold quality
blood vessel layerUBERON:000479792.16gold quality
palpebral conjunctivaUBERON:000181291.89gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3yes5.99

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

357 targeting RNF38, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-8485100.0077.574731
HSA-MIR-3163100.0077.238605
HSA-MIR-3613-3P100.0076.367965
HSA-MIR-4668-3P100.0068.742635
HSA-MIR-200B-3P100.0073.312693
HSA-MIR-200C-3P100.0073.352685
HSA-MIR-429100.0073.442698
HSA-LET-7A-3P100.0074.033932
HSA-LET-7B-3P100.0074.083913
HSA-LET-7F-1-3P100.0074.023928
HSA-MIR-98-3P100.0074.083907
HSA-MIR-4262100.0073.263931
HSA-MIR-4776-3P100.0068.731340
HSA-MIR-4510100.0066.602050
HSA-MIR-6127100.0066.762188
HSA-MIR-6129100.0066.462080
HSA-MIR-6130100.0066.692012
HSA-MIR-6133100.0066.482064
HSA-MIR-548C-3P99.9974.017587
HSA-MIR-366299.9973.825684
HSA-MIR-34A-5P99.9971.211784
HSA-MIR-449A99.9971.051776
HSA-MIR-428299.9975.366408
HSA-MIR-371B-5P99.9975.344759
HSA-MIR-450099.9972.722367
HSA-MIR-32-5P99.9875.211964
HSA-MIR-92A-3P99.9875.211960
HSA-MIR-92B-3P99.9875.251955
HSA-MIR-367-3P99.9874.831819
HSA-MIR-363-3P99.9874.721821

Literature-anchored findings (GeneRIF, showing 10)

  • Cloning and characterization of the RNF38 gene (PMID:12074600)
  • These results suggest RNF38 is an E3 ubiquitin ligase that may play a role in regulating p53. (PMID:23973461)
  • Data show that E3 ubiquitin-protein ligase RNF38 (RNF38) interacts with the nonreceptor tyrosine phosphatase SH2-containing protein tyrosine phosphatase 1 (SHP-1) and induces the polyubiquitination of SHP-1, which leads to destabilization of SHP-1. (PMID:30112836)
  • identified RNF38 as a novel E3 ligase that modifies RUNX1 function without inducing its degradation (PMID:30309654)
  • AHNAK interference restored the hepatocellular carcinoma (HCC) cell invasion and metastasis deprived by RNF38 downregulation. Clinically, elevated RNF38 and transforming growth factor beta receptor 1 (TGFBR1) expression was related to short overall survival (OS) and high cumulative recurrence rates in HCC patients. (PMID:30836988)
  • Long non-coding RNA SNHG5 promotes human hepatocellular carcinoma progression by regulating miR-363-3p/RNF38 axis. (PMID:32329834)
  • Inhibiting microRNA-301b suppresses cell growth and targets RNF38 in cervical carcinoma. (PMID:32643846)
  • RNF38 inhibits osteosarcoma cell proliferation by binding to CRY1. (PMID:34460347)
  • RNF38 suppress growth and metastasis via ubiquitination of ACTN4 in nasopharyngeal carcinoma. (PMID:35568845)
  • Hsa_circ_0097009 regulates proliferation, apoptosis, migration and invasion of hepatocellular carcinoma cells via miR-568/RNF38 axis. (PMID:36598315)

Cross-species orthologs

3 orthologs

OrganismSymbolGene ID
danio_reriornf38ENSDARG00000062055
mus_musculusRnf38ENSMUSG00000035696
rattus_norvegicusRnf38ENSRNOG00000013956

Paralogs (3): RNF6 (ENSG00000127870), RLIM (ENSG00000131263), RNF44 (ENSG00000146083)

Protein

Protein identifiers

E3 ubiquitin-protein ligase RNF38Q9H0F5 (reviewed: Q9H0F5)

Alternative names: RING finger protein 38, RING-type E3 ubiquitin transferase RNF38

All UniProt accessions (1): Q9H0F5

UniProt curated annotations — full annotation on UniProt →

Function. Acts as an E3 ubiquitin-protein ligase able to ubiquitinate p53/TP53 which promotes its relocalization to discrete foci associated with PML nuclear bodies. Exhibits preference for UBE2D2 as a E2 enzyme.

Subcellular location. Nucleus.

Tissue specificity. Widely expressed with highest levels in testis.

Pathway. Protein modification; protein ubiquitination.

Isoforms (5)

UniProt IDNamesCanonical?
Q9H0F5-11yes
Q9H0F5-22
Q9H0F5-33
Q9H0F5-44
Q9H0F5-55

RefSeq proteins (5): NP_073618, NP_919309, NP_919310, NP_919311, NP_919313 (=MANE)

Domains & families (InterPro)

IDNameType
IPR001841Znf_RINGDomain
IPR013083Znf_RING/FYVE/PHDHomologous_superfamily

Pfam: PF13639

UniProt features (25 total): splice variant 5, strand 5, turn 3, sequence conflict 2, helix 2, short sequence motif 2, compositionally biased region 2, chain 1, zinc finger region 1, sequence variant 1, region of interest 1

Structure

Experimental structures (PDB)

6 structures.

PDBMethodResolution (Å)
9Q88X-RAY DIFFRACTION1.2
4V3LX-RAY DIFFRACTION1.53
4V3KX-RAY DIFFRACTION2.04
7OJXX-RAY DIFFRACTION2.4
9Q8YX-RAY DIFFRACTION2.63
1X4JSOLUTION NMR

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q9H0F5-F152.690.14

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 300 (showing top): MYAATNNNNNNNGGC_UNKNOWN, GGTGTGT_MIR329, TGCGCANK_UNKNOWN, CMYB_01, TATTATA_MIR374, AREB6_01, GGGTGGRR_PAX4_03, LINDGREN_BLADDER_CANCER_CLUSTER_2A_DN, CATTTCA_MIR203, MCAATNNNNNGCG_UNKNOWN, chr9p13, TGTGTGA_MIR377, ACATTCC_MIR1_MIR206, TGACATY_UNKNOWN, GOBP_POST_TRANSLATIONAL_PROTEIN_MODIFICATION

GO Biological Process (2): male gonad development (GO:0008584), protein ubiquitination (GO:0016567)

GO Molecular Function (5): zinc ion binding (GO:0008270), ubiquitin protein ligase activity (GO:0061630), protein binding (GO:0005515), transferase activity (GO:0016740), metal ion binding (GO:0046872)

GO Cellular Component (3): nucleus (GO:0005634), nucleoplasm (GO:0005654), sperm flagellum (GO:0036126)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
gonad development1
development of primary male sexual characteristics1
protein modification by small protein conjugation1
transition metal ion binding1
ubiquitin-protein transferase activity1
ubiquitin-like protein ligase activity1
binding1
catalytic activity1
cation binding1
intracellular membrane-bounded organelle1
nuclear lumen1
cellular anatomical structure1
9+2 motile cilium1

Protein interactions and networks

STRING

902 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
RNF38GNEQ9Y223952
RNF38UBE2D2P51669899
RNF38NANSQ9NR45575
RNF38UAP1Q16222569
RNF38TMEM169Q96HH4497
RNF38UBBP02248496
RNF38BIRC7Q96CA5438
RNF38SHBQ15464434
RNF38TRIM31Q9BZY9434
RNF38BSNQ9UPA5433
RNF38RBBP6Q7Z6E9425
RNF38RNF4P78317422
RNF38FAM174AQ8TBP5422
RNF38OPCMLQ14982403
RNF38NREPQ16612400

IntAct

54 interactions, top by confidence:

ABTypeScore
RNF38RNF208psi-mi:“MI:0915”(physical association)0.560
CYSRT1RNF38psi-mi:“MI:0915”(physical association)0.560
OXER1RNF38psi-mi:“MI:0915”(physical association)0.560
LASP1RNF38psi-mi:“MI:0915”(physical association)0.560
KRTAP8-1RNF38psi-mi:“MI:0915”(physical association)0.560
KRTAP6-2RNF38psi-mi:“MI:0915”(physical association)0.560
KPRPRNF38psi-mi:“MI:0915”(physical association)0.560
KRTAP11-1RNF38psi-mi:“MI:0915”(physical association)0.560
KRTAP10-8RNF38psi-mi:“MI:0915”(physical association)0.560
KRTAP21-2RNF38psi-mi:“MI:0915”(physical association)0.560
KRTAP7-1RNF38psi-mi:“MI:0915”(physical association)0.560
KRTAP19-5RNF38psi-mi:“MI:0915”(physical association)0.560
RNF38psi-mi:“MI:0915”(physical association)0.490
NEDD4RNF38psi-mi:“MI:0407”(direct interaction)0.440
YAP1RNF38psi-mi:“MI:0407”(direct interaction)0.440
KPNA4RNF38psi-mi:“MI:0407”(direct interaction)0.440
RNF38bipApsi-mi:“MI:0915”(physical association)0.370
RNF38iglC2psi-mi:“MI:0915”(physical association)0.370
UBE2D1RNF38psi-mi:“MI:0915”(physical association)0.370
RNF38UBE2D2psi-mi:“MI:0915”(physical association)0.370
UBE2D3RNF38psi-mi:“MI:0915”(physical association)0.370
RNF38UBE2Hpsi-mi:“MI:0915”(physical association)0.370
RNF38UBE2D4psi-mi:“MI:0915”(physical association)0.370
DZIP3RNF38psi-mi:“MI:0915”(physical association)0.370
RNF114RNF38psi-mi:“MI:0915”(physical association)0.370
RNF38DTX3psi-mi:“MI:0915”(physical association)0.370
ZDHHC17RNF38psi-mi:“MI:0915”(physical association)0.370

BioGRID (125): RNF38 (Two-hybrid), RNF38 (Biochemical Activity), RNF38 (Reconstituted Complex), UBE2D2 (Reconstituted Complex), UBC (Biochemical Activity), RNF38 (Affinity Capture-RNA), RNF38 (Reconstituted Complex), RNF38 (Affinity Capture-Western), PTPN6 (Affinity Capture-Western), RNF38 (Affinity Capture-MS), AHNAK (Affinity Capture-MS), TRIM21 (Affinity Capture-MS), DCD (Affinity Capture-MS), SPIDR (Affinity Capture-MS), CD109 (Affinity Capture-MS)

ESM2 similar proteins: A2AFE9, A2X0Q6, A3A2Z8, A5PJK7, B1ATL7, C7IW64, O65685, O94602, P03413, P11821, P38128, P80074, Q01196, Q03347, Q08775, Q0V9R0, Q10108, Q13761, Q2HRB6, Q5R476, Q5UQP5, Q63046, Q66J97, Q6AWY2, Q6F2E2, Q6NRV8, Q6PF39, Q6ZNA4, Q7L0R7, Q84JP1, Q8CFA7, Q8LFU0, Q8VY64, Q90ZT7, Q93ZH2, Q945M9, Q99ML9, Q9D1Z2, Q9E6P2, Q9FGD6

Diamond homologs: A5WWA0, E9QAU8, O22197, O43567, O49500, O54965, O64763, O80927, P0CH02, P0CH30, P0DPR2, Q06003, Q07G42, Q08CG8, Q08D68, Q0V9R0, Q0VD51, Q0WPW5, Q3T0W3, Q3U2C5, Q3UHJ8, Q4KLR8, Q4V7B8, Q566M8, Q5DTZ6, Q5M974, Q5NCP0, Q5R476, Q5RCV8, Q5SSZ7, Q5XIL0, Q641J8, Q66HG0, Q66J97, Q67YI6, Q68DV7, Q69U49, Q6AVN2, Q6AXU4, Q6GPV5

SIGNOR signaling

2 interactions.

AEffectBMechanism
Ub:E2“up-regulates activity”RNF38ubiquitination
RNF38“down-regulates activity”TP53ubiquitination

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 27 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

PathwayPartnersFoldFDR
Keratinization618.6×2e-05
Antigen processing: Ubiquitination & Proteasome degradation816.5×7e-07

GO biological processes:

GO termPartnersFoldFDR
protein K48-linked ubiquitination544.4×3e-06
protein polyubiquitination636.5×6e-07
ubiquitin-dependent protein catabolic process727.4×4e-07
protein ubiquitination613.1×1e-04

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance58
Likely benign1
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1953 predictions. Top by Δscore:

VariantEffectΔscore
9:36339810:TTTGC:Tacceptor_gain1.0000
9:36339811:TTGC:Tacceptor_gain1.0000
9:36339812:TGC:Tacceptor_gain1.0000
9:36339812:TGCC:Tacceptor_loss1.0000
9:36339813:GC:Gacceptor_gain1.0000
9:36339814:CC:Cacceptor_gain1.0000
9:36339815:C:CAacceptor_loss1.0000
9:36339815:C:CCacceptor_gain1.0000
9:36339816:T:Gacceptor_loss1.0000
9:36339818:C:CTacceptor_gain1.0000
9:36344826:A:ACdonor_gain1.0000
9:36344826:ACTT:Adonor_loss1.0000
9:36344827:C:CCdonor_gain1.0000
9:36344828:TTACA:Tdonor_loss1.0000
9:36344829:TACAA:Tdonor_loss1.0000
9:36344830:A:ACdonor_gain1.0000
9:36344830:AC:Adonor_loss1.0000
9:36344831:C:CAdonor_gain1.0000
9:36344831:CA:Cdonor_gain1.0000
9:36344831:CAA:Cdonor_gain1.0000
9:36344831:CAAA:Cdonor_gain1.0000
9:36344831:CAAAG:Cdonor_gain1.0000
9:36344954:C:CCacceptor_gain1.0000
9:36344954:CT:Cacceptor_loss1.0000
9:36344961:G:Tacceptor_gain1.0000
9:36351110:CTAA:Cdonor_loss1.0000
9:36351111:TAA:Tdonor_loss1.0000
9:36351112:AAC:Adonor_loss1.0000
9:36351114:C:CTdonor_loss1.0000
9:36352740:A:ACdonor_gain1.0000

AlphaMissense

3328 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
9:36339789:C:GR504P1.000
9:36339791:G:CC503W1.000
9:36339792:C:AC503F1.000
9:36339792:C:GC503S1.000
9:36339792:C:TC503Y1.000
9:36339793:A:GC503R1.000
9:36339793:A:TC503S1.000
9:36339795:A:CI502S1.000
9:36339795:A:TI502N1.000
9:36339798:G:CP501R1.000
9:36339798:G:TP501Q1.000
9:36339799:G:AP501S1.000
9:36339799:G:TP501T1.000
9:36339800:G:CC500W1.000
9:36339801:C:AC500F1.000
9:36339801:C:GC500S1.000
9:36339801:C:TC500Y1.000
9:36339802:A:CC500G1.000
9:36339802:A:GC500R1.000
9:36339802:A:TC500S1.000
9:36342329:A:GL494P1.000
9:36342329:A:TL494H1.000
9:36342331:C:AW493C1.000
9:36342331:C:GW493C1.000
9:36342332:C:GW493S1.000
9:36342333:A:GW493R1.000
9:36342333:A:TW493R1.000
9:36342341:A:TV490D1.000
9:36342343:A:CC489W1.000
9:36342344:C:AC489F1.000

dbSNP variants (sampled 300 via entrez): RS1000017056 (9:36419275 T>G), RS1000056828 (9:36484128 T>G), RS1000073931 (9:36460464 C>G), RS1000076679 (9:36471873 G>A), RS1000081663 (9:36481939 G>A), RS1000085255 (9:36466127 T>C), RS1000092040 (9:36415427 TTTTG>T), RS1000116341 (9:36357543 T>C), RS1000143052 (9:36415646 T>C), RS1000152024 (9:36389728 T>C), RS1000165998 (9:36367213 G>C,T), RS1000184878 (9:36484998 C>G), RS1000189934 (9:36406921 A>G), RS1000223180 (9:36373234 T>C), RS1000227469 (9:36454827 A>C,G)

Disease associations

OMIM: gene MIM:612488 | 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):

StudyTraitp-value
GCST002815_5Bipolar disorder (inflammation and infection response interaction)6.000000e-06

EFO canonical traits (1, from GWAS)

EFO IDTrait name
EFO:0007050HSV1 seropositivity

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

32 total (human), top 30 by PubMed support.

ChemicalActions (top 5)PubMed papers
Tobacco Smoke Pollutiondecreases methylation, increases expression2
Valproic Acidaffects expression, decreases expression2
Cyclosporinedecreases expression, increases expression2
aristolochic acid Idecreases expression1
GSK-J4increases expression1
bisphenol Aincreases expression1
beta-lapachonedecreases expression1
tris(1,3-dichloro-2-propyl)phosphateincreases expression1
sodium arsenitedecreases expression1
di-n-butylphosphoric acidaffects expression1
monomethylarsonous acidincreases expression1
erastinaffects cotreatment, increases expression1
abrinedecreases expression1
bisphenol Sincreases expression1
(+)-JQ1 compoundincreases expression1
Sunitinibdecreases expression1
Acetaminophenincreases expression1
Atrazinedecreases expression1
Cadmiumdecreases expression, increases abundance1
Doxorubicindecreases expression1
Doxycyclineincreases expression, affects cotreatment1
Endosulfanincreases expression1
Formaldehydedecreases expression1
Leadaffects splicing1
Testosteroneincreases expression1
Thiramincreases expression1
Urethaneincreases expression1
7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxidedecreases expression1
Isotretinoinincreases expression1
Antirheumatic Agentsdecreases expression1

Clinical trials (associated diseases)

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

No linked Atlas pages yet — the cross-entity mesh grows as the corpus expands.