RNF17

Summary

RNF17 (ring finger protein 17, HGNC:10060) is a protein-coding gene on chromosome 13q12.12, encoding RING finger protein 17 (Q9BXT8). Seems to be involved in regulation of transcriptional activity of MYC.

This gene is similar to a mouse gene that encodes a testis-specific protein containing a RING finger domain. Alternatively spliced transcript variants encoding different isoforms have been found.

Source: NCBI Gene 56163 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 221 total — 3 pathogenic, 2 likely-pathogenic
• MANE Select transcript: NM_031277

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:10060
Approved symbol	RNF17
Name	ring finger protein 17
Location	13q12.12
Locus type	gene with protein product
Status	Approved
Aliases	Mmip-2, SPATA23, FLJ11045
Ensembl gene	ENSG00000132972
Ensembl biotype	protein_coding
OMIM	605793
Entrez	56163

Gene structure

Transcript identifiers

Ensembl transcripts: 5 — 4 protein_coding, 1 protein_coding_CDS_not_defined

ENST00000255324, ENST00000255325, ENST00000255326, ENST00000339524, ENST00000418120

RefSeq mRNA: 2 — MANE Select: NM_031277 NM_001184993, NM_031277

CCDS: CCDS9308

Canonical transcript exons

ENST00000255324 — 36 exons

Exon	Start	End
ENSE00000906525	24879187	24879295
ENSE00000906526	24876997	24877186
ENSE00001144865	24874114	24874249
ENSE00001144871	24870571	24870739
ENSE00001144876	24868600	24868716
ENSE00001144882	24866144	24866203
ENSE00001144895	24861268	24861387
ENSE00001144905	24853855	24854144
ENSE00001144911	24851456	24851571
ENSE00001144918	24850341	24850443
ENSE00001144924	24844961	24845079
ENSE00001375546	24864873	24864998
ENSE00001391074	24862713	24862793
ENSE00001490241	24879737	24879921
ENSE00001646722	24799395	24799584
ENSE00001671772	24830484	24830599
ENSE00001687093	24796137	24796295
ENSE00001695592	24802381	24802571
ENSE00001706074	24825619	24825772
ENSE00001729598	24842041	24842161
ENSE00001731008	24843744	24843971
ENSE00001767298	24800366	24800534
ENSE00001786297	24831858	24831978
ENSE00001843925	24764169	24764333
ENSE00002711173	24859001	24859164
ENSE00003459182	24774813	24774904
ENSE00003471912	24789698	24789772
ENSE00003475335	24767272	24767366
ENSE00003498903	24804288	24804429
ENSE00003552207	24779667	24779747
ENSE00003562074	24778295	24778406
ENSE00003570612	24787988	24788159
ENSE00003573459	24781844	24781944
ENSE00003641245	24844652	24844802
ENSE00003642024	24789348	24789424
ENSE00003657384	24793042	24793346

Expression profiles

Bgee: expression breadth ubiquitous, 142 present calls, max score 94.25.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.3202 / max 97.4091, expressed in 55 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
134448	0.3202	55

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	94.25	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	93.31	gold quality
right testis	UBERON:0004534	90.03	gold quality
left testis	UBERON:0004533	89.01	gold quality
testis	UBERON:0000473	87.99	gold quality
secondary oocyte	CL:0000655	79.12	gold quality
sperm	CL:0000019	78.81	gold quality
male germ cell	CL:0000015	77.14	gold quality
buccal mucosa cell	CL:0002336	71.59	silver quality
oocyte	CL:0000023	64.94	gold quality
tibialis anterior	UBERON:0001385	60.59	silver quality
mucosa of urinary bladder	UBERON:0001259	60.28	gold quality
pancreatic ductal cell	CL:0002079	60.27	silver quality
ileal mucosa	UBERON:0000331	60.14	silver quality
diaphragm	UBERON:0001103	60.00	gold quality
adult organism	UBERON:0007023	59.92	gold quality
endothelial cell	CL:0000115	59.31	gold quality
epithelium of nasopharynx	UBERON:0001951	58.76	gold quality
deltoid	UBERON:0001476	58.04	gold quality
quadriceps femoris	UBERON:0001377	57.21	gold quality
decidua	UBERON:0002450	56.55	gold quality
vastus lateralis	UBERON:0001379	55.92	gold quality
myocardium	UBERON:0002349	55.33	gold quality
mucosa of transverse colon	UBERON:0004991	55.27	gold quality
upper leg skin	UBERON:0004262	54.56	gold quality
vena cava	UBERON:0004087	54.44	gold quality
cortical plate	UBERON:0005343	52.83	gold quality
hair follicle	UBERON:0002073	52.43	gold quality
substantia nigra pars compacta	UBERON:0001965	51.60	gold quality
cardiac muscle of right atrium	UBERON:0003379	51.32	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	7.17

Regulation

Is transcription factor: no

Literature-anchored findings (GeneRIF, showing 3)

• TDRD4 mRNA is expressed in a subset of liver cancers, and TDRD4 is a candidate CT antigen for liver cancer. (PMID:21515969)
• TDRD4 showed significant up-regulation in invasive ductal breast carcinoma. (PMID:24377578)
• Further mining of the UBE2U interactome uncovered its cognate E3 RNF17 as a novel factor that, via the radiosensitivity, immunodeficiency, dysmorphic features, and learning difficulties (RIDDLE) syndrome protein RNF168, enforces DNA damage responses. (PMID:27903633)

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	rnf17	ENSDARG00000056387
mus_musculus	Rnf17	ENSMUSG00000000365
rattus_norvegicus	Rnf17	ENSRNOG00000008059
caenorhabditis_elegans		WBGENE00012684

Protein

Protein identifiers

RING finger protein 17 — Q9BXT8 (reviewed: Q9BXT8)

Alternative names: Tudor domain-containing protein 4

All UniProt accessions (3): Q9BXT8, Q5T2J8, Q5T6R1

UniProt curated annotations — full annotation on UniProt →

Function. Seems to be involved in regulation of transcriptional activity of MYC. In vitro, inhibits DNA-binding activity of Mad-MAX heterodimers. Can recruit Mad transcriptional repressors (MXD1, MXD3, MXD4 and MXI1) to the cytoplasm. May be involved in spermiogenesis.

Subunit / interactions. Interacts with MXD1, MXD3, MXD4, MXI1 and PIWIL1. Self-associates.

Subcellular location. Cytoplasm. Nucleus.

Tissue specificity. Testis specific.

Isoforms (5)

UniProt ID	Names	Canonical?
Q9BXT8-3	1	yes
Q9BXT8-1	2
Q9BXT8-2	3
Q9BXT8-4	4
Q9BXT8-5	5

RefSeq proteins (2): NP_001171922, NP_112567* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001841	Znf_RING	Domain
IPR002999	Tudor	Domain
IPR017907	Znf_RING_CS	Conserved_site
IPR035437	SNase_OB-fold_sf	Homologous_superfamily
IPR047845	RNF17-like_TUDOR_rpt1	Domain
IPR047847	RNF17-like_TUDOR_rpt2	Domain
IPR047848	RNF17-like_TUDOR_rpt3	Domain
IPR047849	RNF17-like_TUDOR_rpt4	Domain
IPR047850	RNF17-like_TUDOR_rpt5	Domain

Pfam: PF00567

UniProt features (33 total): sequence variant 7, splice variant 6, strand 6, domain 4, helix 2, turn 2, region of interest 2, chain 1, sequence conflict 1, zinc finger region 1, modified residue 1

Structure

Experimental structures (PDB)

1 structures.

PDB	Method	Resolution (Å)
2EQK	SOLUTION NMR

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9BXT8-F1	69.25	0.18

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): 234

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 67 (showing top): GOBP_MALE_GAMETE_GENERATION, CEBPB_01, SHETH_LIVER_CANCER_VS_TXNIP_LOSS_PAM5, WTGAAAT_UNKNOWN, GOBP_CELLULAR_PROCESS_INVOLVED_IN_REPRODUCTION_IN_MULTICELLULAR_ORGANISM, HFH1_01, GOBP_DEVELOPMENTAL_PROCESS_INVOLVED_IN_REPRODUCTION, FREAC7_01, ACEVEDO_METHYLATED_IN_LIVER_CANCER_DN, NKX3A_01, WEBER_METHYLATED_ICP_IN_SPERM_DN, ACTWSNACTNY_UNKNOWN, YKACATTT_UNKNOWN, MATZUK_SPERMATID_DIFFERENTIATION, P53_02

GO Biological Process (3): spermatid development (GO:0007286), spermatogenesis (GO:0007283), cell differentiation (GO:0030154)

GO Molecular Function (3): zinc ion binding (GO:0008270), identical protein binding (GO:0042802), metal ion binding (GO:0046872)

GO Cellular Component (2): nucleus (GO:0005634), cytoplasm (GO:0005737)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
germ cell development	1
spermatid differentiation	1
developmental process involved in reproduction	1
male gamete generation	1
cellular developmental process	1
transition metal ion binding	1
protein binding	1
cation binding	1
intracellular membrane-bounded organelle	1
intracellular anatomical structure	1
cellular anatomical structure	1

Protein interactions and networks

STRING

1090 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
RNF17	PIWIL2	Q8TC59	785
RNF17	PIWIL1	Q96J94	753
RNF17	STK31	Q9BXU1	613
RNF17	MOV10L1	Q9BXT6	603
RNF17	DAZL	Q92904	599
RNF17	MAEL	Q96JY0	569
RNF17	TDRD12	Q587J7	553
RNF17	TDRD9	Q8NDG6	549
RNF17	GARIN2	Q8N9W8	532
RNF17	ROPN1L	Q96C74	531
RNF17	DDX4	Q9NQI0	531
RNF17	DMRT1	Q9Y5R6	528
RNF17	UBE2U	Q5VVX9	524
RNF17	PIWIL4	Q7Z3Z4	513
RNF17	TDRD5	Q8NAT2	504

IntAct

4 interactions, top by confidence:

A	B	Type	Score
UBE2U	RNF17	psi-mi:“MI:0915”(physical association)	0.370
CBX4		psi-mi:“MI:0914”(association)	0.350
CDC5L		psi-mi:“MI:0914”(association)	0.350

BioGRID (14): RNF17 (Affinity Capture-MS), EPPK1 (Affinity Capture-MS), MSRA (Affinity Capture-MS), NBPF10 (Affinity Capture-MS), NFX1 (Affinity Capture-MS), PRMT1 (Affinity Capture-MS), RNF17 (Affinity Capture-MS), RNF17 (Affinity Capture-MS), RNF17 (Affinity Capture-MS), RNF17 (Cross-Linking-MS (XL-MS)), RNF17 (Cross-Linking-MS (XL-MS)), RNF17 (Protein-RNA), THOC2 (Cross-Linking-MS (XL-MS)), RNF17 (Two-hybrid)

ESM2 similar proteins: A0JM98, A1L1H3, A6NAF9, A6QLE1, A9CPT4, B5MCY1, D2H0H6, D2H3M0, D4A7V9, E1BPH3, E1C3S7, E2QTD3, E2RDV1, E7FDW8, F1R237, O60522, P57075, P61407, P97874, Q14B46, Q1L981, Q4R3G4, Q58EK5, Q5DTW2, Q5JTW2, Q5M7P8, Q5RAH6, Q5VCS6, Q5VZ19, Q5XGX5, Q61846, Q68DX3, Q6NU04, Q80VK6, Q8K1H1, Q8NAT2, Q8NHU6, Q90WE3, Q99KY4, Q99MV1

Diamond homologs: A3KMI0, B0XDC4, B3M383, B3P3W1, B4GEU5, B4HLH4, B4JT42, B4K5R2, B4LX81, B4NBB0, B4PRJ9, B8A4F4, D4A2Z8, F4HYJ7, F4I9Q5, F4IDQ6, F4IJV4, F4ILR7, F4IM84, F4INY4, F4JMJ3, F4JRJ6, O42945, O45244, O60114, O60231, O70133, O94536, P0C7L7, P15938, P20095, P24785, P36009, P43329, P45018, P53131, Q05B79, Q06698, Q08211, Q09530

SIGNOR signaling

1 interactions.

A	Effect	B	Mechanism
Ub:E2	“up-regulates activity”	RNF17	ubiquitination

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	3
Likely pathogenic	2
Uncertain significance	163
Likely benign	20
Benign	13

Top pathogenic / likely-pathogenic (5)

Variant ID	HGVS	Classification
158211	NM_018451.5(CPAP):c.3448C>T (p.Gln1150Ter)	Pathogenic
18417	NM_018451.5(CPAP):c.3302-1G>C	Pathogenic
3661127	NM_018451.5(CPAP):c.3682del (p.His1228fs)	Pathogenic
3778765	NM_018451.5(CPAP):c.3765_3768dup (p.Pro1257fs)	Likely pathogenic
417856	NM_018451.5(CPAP):c.3367-1G>A	Likely pathogenic

SpliceAI

6700 predictions. Top by Δscore:

Variant	Effect	Δscore
13:24764263:G:GT	donor_gain	1.0000
13:24764315:A:T	donor_gain	1.0000
13:24774902:G:GT	donor_gain	1.0000
13:24774902:GAC:G	donor_gain	1.0000
13:24774905:G:GG	donor_gain	1.0000
13:24778395:GCT:G	donor_gain	1.0000
13:24778423:TCATG:T	donor_gain	1.0000
13:24779730:T:G	donor_gain	1.0000
13:24779748:G:GG	donor_gain	1.0000
13:24781841:CA:C	acceptor_loss	1.0000
13:24781842:A:AG	acceptor_gain	1.0000
13:24781842:A:AT	acceptor_loss	1.0000
13:24781842:AG:A	acceptor_gain	1.0000
13:24781843:G:GT	acceptor_gain	1.0000
13:24781843:GG:G	acceptor_gain	1.0000
13:24781843:GGC:G	acceptor_gain	1.0000
13:24781843:GGCA:G	acceptor_gain	1.0000
13:24781843:GGCAC:G	acceptor_gain	1.0000
13:24781941:CCAGG:C	donor_loss	1.0000
13:24781944:GGT:G	donor_loss	1.0000
13:24781945:G:T	donor_loss	1.0000
13:24781946:T:A	donor_loss	1.0000
13:24789426:T:G	donor_loss	1.0000
13:24789770:AAAG:A	donor_loss	1.0000
13:24789772:AG:A	donor_loss	1.0000
13:24789773:G:GG	donor_gain	1.0000
13:24789773:GTA:G	donor_loss	1.0000
13:24789774:TAAG:T	donor_loss	1.0000
13:24789775:A:AG	donor_loss	1.0000
13:24789776:AG:A	donor_loss	1.0000

AlphaMissense

10749 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
13:24850363:T:A	W1042R	0.999
13:24850363:T:C	W1042R	0.999
13:24850365:G:C	W1042C	0.998
13:24850365:G:T	W1042C	0.998
13:24862725:T:A	W1303R	0.998
13:24862725:T:C	W1303R	0.998
13:24859120:T:A	W1244R	0.997
13:24859120:T:C	W1244R	0.997
13:24877118:T:A	W1569R	0.997
13:24877118:T:C	W1569R	0.997
13:24844755:T:A	W979R	0.996
13:24844755:T:C	W979R	0.996
13:24859126:C:A	R1246S	0.996
13:24802490:T:C	L623P	0.995
13:24825730:G:C	A735P	0.995
13:24825751:T:A	W742R	0.995
13:24825751:T:C	W742R	0.995
13:24825760:G:C	A745P	0.995
13:24831909:T:A	W805R	0.995
13:24831909:T:C	W805R	0.995
13:24851556:C:A	A1102D	0.995
13:24859127:G:C	R1246P	0.995
13:24868685:T:A	V1416D	0.995
13:24874157:A:C	R1497S	0.995
13:24874157:A:T	R1497S	0.995
13:24800509:T:C	L578S	0.994
13:24825731:C:A	A735D	0.994
13:24854094:T:A	V1187D	0.994
13:24861364:T:C	C1291R	0.994
13:24874158:G:C	A1498P	0.994

dbSNP variants (sampled 300 via entrez): RS1000027828 (13:24758898 A>T), RS1000041429 (13:24752085 G>A), RS1000058690 (13:24748588 T>C), RS1000058935 (13:24830561 C>T), RS1000083146 (13:24853285 A>C,G), RS1000097381 (13:24775627 T>A), RS1000120672 (13:24763641 C>A), RS1000157930 (13:24844440 T>A,C), RS1000175378 (13:24837993 A>G), RS1000188607 (13:24837023 G>C,T), RS1000203483 (13:24782359 T>G), RS1000223588 (13:24789023 G>C,T), RS1000223878 (13:24764144 G>A,C), RS1000244077 (13:24788232 C>A,T), RS1000250069 (13:24817700 C>G,T)

Disease associations

OMIM: gene MIM:605793 | disease phenotypes: MIM:251200, MIM:608393, MIM:613676, MIM:208085

GenCC curated gene-disease

Mondo (4): microcephaly 1, primary, autosomal recessive (MONDO:0009617), microcephaly 6, primary, autosomal recessive (MONDO:0012029), Seckel syndrome 4 (MONDO:0013358), arthrogryposis, renal dysfunction, and cholestasis 1 (MONDO:0008822)

Orphanet (4): Autosomal recessive primary microcephaly (Orphanet:2512), Seckel syndrome (Orphanet:808), Arthrogryposis-renal dysfunction-cholestasis syndrome (Orphanet:2697), Premature chromosome condensation with microcephaly and intellectual disability (Orphanet:52183)

HPO phenotypes

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

GWAS associations

0 associations (top):

MeSH disease descriptors (2)

Descriptor	Name	Tree numbers
C565384	Microcephaly, Primary Autosomal Recessive, 1 (supp.)
C564247	Microcephaly, Primary Autosomal Recessive, 6 (supp.)

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

9 total (human), top 9 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Benzo(a)pyrene	decreases expression, increases methylation	2
FR900359	increases phosphorylation	1
pirinixic acid	affects binding, increases activity, increases expression	1
aflatoxin B2	increases methylation	1
CGP 52608	affects binding, increases reaction	1
abrine	decreases expression	1
Acetaminophen	increases expression	1
Silicon Dioxide	decreases expression	1
Valproic Acid	increases methylation	1

Clinical trials (associated diseases)

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