RDM1

Summary

RDM1 (RAD52 motif containing 1, HGNC:19950) is a protein-coding gene on chromosome 17q12, encoding RAD52 motif-containing protein 1 (Q8NG50). May confer resistance to the antitumor agent cisplatin.

This gene encodes a protein involved in the cellular response to cisplatin, a drug commonly used in chemotherapy. The protein encoded by this gene contains two motifs: a motif found in RAD52, a protein that functions in DNA double-strand breaks and homologous recombination, and an RNA recognition motif (RRM) that is not found in RAD52. The RAD52 motif region in RAD52 is important for protein function and may be involved in DNA binding or oligomerization. Alternatively spliced transcript variants encoding different isoforms have been reported.

Source: NCBI Gene 201299 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 36 total
• MANE Select transcript: NM_145654

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:19950
Approved symbol	RDM1
Name	RAD52 motif containing 1
Location	17q12
Locus type	gene with protein product
Status	Approved
Aliases	MGC33977
Ensembl gene	ENSG00000278023
Ensembl biotype	protein_coding
OMIM	612896
Entrez	201299

Gene structure

Transcript identifiers

Ensembl transcripts: 14 — 9 protein_coding, 5 nonsense_mediated_decay

ENST00000612980, ENST00000613308, ENST00000615024, ENST00000615288, ENST00000615378, ENST00000616596, ENST00000617591, ENST00000618511, ENST00000619193, ENST00000619262, ENST00000619368, ENST00000619828, ENST00000619876, ENST00000620284

RefSeq mRNA: 9 — MANE Select: NM_145654 NM_001034836, NM_001163120, NM_001163121, NM_001163122, NM_001163124, NM_001163125, NM_001163130, NM_001330194, NM_145654

CCDS: CCDS11301, CCDS42299, CCDS54108, CCDS54109, CCDS54110, CCDS54111, CCDS59280, CCDS59281, CCDS82109

Canonical transcript exons

ENST00000618461 — 0 exons

Expression profiles

Bgee: expression breadth ubiquitous, 130 present calls, max score 85.54.

FANTOM5 (CAGE): breadth broad, TPM avg 1.0944 / max 32.5324, expressed in 520 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
165406	0.7202	396
165407	0.3742	204

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	85.54	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	82.64	gold quality
right testis	UBERON:0004534	80.33	gold quality
left testis	UBERON:0004533	80.30	gold quality
testis	UBERON:0000473	79.91	gold quality
ventricular zone	UBERON:0003053	76.88	gold quality
ganglionic eminence	UBERON:0004023	73.12	gold quality
mucosa of transverse colon	UBERON:0004991	70.08	gold quality
duodenum	UBERON:0002114	66.07	gold quality
lymph node	UBERON:0000029	65.47	gold quality
rectum	UBERON:0001052	65.10	gold quality
placenta	UBERON:0001987	64.74	gold quality
vermiform appendix	UBERON:0001154	63.37	gold quality
lower esophagus mucosa	UBERON:0035834	61.34	gold quality
endometrium	UBERON:0001295	61.09	gold quality
granulocyte	CL:0000094	59.00	gold quality
nucleus accumbens	UBERON:0001882	58.56	gold quality
blood	UBERON:0000178	57.78	gold quality
calcaneal tendon	UBERON:0003701	57.04	gold quality
hypothalamus	UBERON:0001898	55.95	gold quality
transverse colon	UBERON:0001157	55.08	gold quality
caudate nucleus	UBERON:0001873	55.03	gold quality
amygdala	UBERON:0001876	54.71	gold quality
putamen	UBERON:0001874	54.68	gold quality
esophagus mucosa	UBERON:0002469	54.46	gold quality
temporal lobe	UBERON:0001871	54.33	gold quality
anterior cingulate cortex	UBERON:0009835	54.16	gold quality
smooth muscle tissue	UBERON:0001135	54.13	gold quality
tonsil	UBERON:0002372	53.98	gold quality
prefrontal cortex	UBERON:0000451	53.93	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	1.73

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

6 targeting RDM1, 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-4688	99.48	64.68	828
HSA-MIR-6814-5P	99.03	66.68	1273
HSA-MIR-4477A	98.83	69.75	2952
HSA-MIR-645	97.28	66.30	486
HSA-MIR-3189-3P	96.80	66.34	896
HSA-MIR-10401-3P	91.66	66.01	97

Literature-anchored findings (GeneRIF, showing 9)

• RDM1 recognizes DNA distortions induced by cisplatin-DNA adducts in vitro; possible role in spermatogenesis (PMID:15611051)
• The identification of 11 human cDNAs encoding RDM1 protein isoforms which is generated by alternative pre-mRNA splicing and differential usage of two translational start sites. (PMID:17905820)
• Due to its similarity to RAD52, we hypothesized that RDM1 potentially repairs DNA doublestrand breaks arising through DNA replication. (PMID:29845285)
• Knockdown of RDM1 in lung adenocarcinoma cells reduces cell proliferation and promotes apoptosis, consistent with the role RDM1 in the overexpression experiments. Xenograft mouse model shows stable knockdown of RDM1 significantly inhibits lung adenocarcinoma tumor growth. These in vitro and in vivo results conclude that RDM1 plays an oncogenic role in human lung adenocarcinoma. (PMID:30069034)
• RDM1 promotes critical processes in breast cancer tumorigenesis. (PMID:31222930)
• Loss of RDM1 enhances hepatocellular carcinoma progression via p53 and Ras/Raf/ERK pathways. (PMID:31670863)
• RDM1 plays an oncogenic role in human ovarian carcinoma cells. (PMID:32501118)
• Association of RDM1 with osteosarcoma progression via cell cycle and MEK/ERK signalling pathway regulation. (PMID:34264012)
• Correlation analysis of RDM1 gene with immune infiltration and clinical prognosis of hepatocellular carcinoma. (PMID:34435618)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	rdm1	ENSDARG00000038186
mus_musculus	Rdm1	ENSMUSG00000010362
rattus_norvegicus	Rdm1	ENSRNOG00000020751

Protein

Protein identifiers

RAD52 motif-containing protein 1 — Q8NG50 (reviewed: Q8NG50)

Alternative names: RAD52 homolog B

All UniProt accessions (2): Q8NG50, B4DZ74

UniProt curated annotations — full annotation on UniProt →

Function. May confer resistance to the antitumor agent cisplatin. Binds to DNA and RNA.

Subunit / interactions. Homodimer.

Subcellular location. Nucleus. Cytoplasm. Nucleolus Cytoplasm. PML body. Cajal body.

Tissue specificity. Expressed in testis.

Domain organisation. C-terminal half (amino acids 134-284) contains cytoplasmic retention domains as well as determinants involved in its stress-induced nucleolar accumulation.

Induction. Heat-shock stress up-regulated mRNA expression of isoform 10 and isoform 11. Heat-shock stress down-regulated short N-terminal mRNA expression of isoform 2, isoform 4, isoform 6 and isoform 9.

Miscellaneous. Produced by alternative promoter usage. Produced by alternative promoter usage. Produced by alternative splicing of isoform 1. Produced by alternative splicing of isoform 2. Produced by alternative splicing of isoform 1. Produced by alternative splicing of isoform 2. Produced by alternative splicing of isoform 1. Produced by alternative splicing of isoform 1. Produced by alternative splicing of isoform 2. Produced by alternative splicing of isoform 1. In cells exposed to a mild heat schock. Produced by alternative splicing of isoform 2. In cells exposed to a mild heat schock.

Isoforms (12)

UniProt ID	Names	Canonical?
Q8NG50-1	1, RDM1alpha, Long N-terminal form	yes
Q8NG50-2	2, DeltaN-RDM1alpha, Short N-terminal form
Q8NG50-3	3, RDM1beta
Q8NG50-4	4, DeltaN-RDM1beta
Q8NG50-5	5, RDM1gamma
Q8NG50-6	6, DeltaN-RDM1gamma
Q8NG50-7	7, RDM1delta
Q8NG50-8	8, RDM1epsilon
Q8NG50-9	9, DeltaN-RDM1epsilon
Q8NG50-10	10, RDM1zeta
Q8NG50-11	11, DeltaN-RDM1zeta
Q8NG50-12	12

RefSeq proteins (9): NP_001030008, NP_001156592, NP_001156593, NP_001156594, NP_001156596, NP_001156597, NP_001156602, NP_001317123, NP_663629* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR000504	RRM_dom	Domain
IPR012677	Nucleotide-bd_a/b_plait_sf	Homologous_superfamily
IPR034200	RDM1_RRM	Domain
IPR035979	RBD_domain_sf	Homologous_superfamily
IPR040224	RDM1	Family
IPR057652	DSRM_RDM1	Domain

Pfam: PF00076, PF25517

UniProt features (17 total): splice variant 8, sequence variant 2, mutagenesis site 2, region of interest 2, chain 1, domain 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8NG50-F1	77.29	0.53

Functional residue map

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

Mutagenesis-validated functional residues (2):

Position	Phenotype
98–100	reduces its nuclear and nucleolar accumulation. increases its cytoplasmic accumulation.
120–122	does not affect its subcellular distribution.

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 94 (showing top): GSE45365_CTRL_VS_MCMV_INFECTION_NK_CELL_UP, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_UP, GRAESSMANN_RESPONSE_TO_MC_AND_DOXORUBICIN_UP, KAUFFMANN_DNA_REPAIR_GENES, IVANOVA_HEMATOPOIESIS_STEM_CELL_SHORT_TERM, FISCHER_DREAM_TARGETS, NUYTTEN_EZH2_TARGETS_DN, GOCC_CAJAL_BODY, GOCC_NUCLEAR_BODY, GOCC_PML_BODY, GOCC_RIBONUCLEOPROTEIN_GRANULE, ZHENG_BOUND_BY_FOXP3, MARSON_BOUND_BY_FOXP3_UNSTIMULATED, MARSON_BOUND_BY_E2F4_UNSTIMULATED, GOCC_NUCLEOLUS

GO Biological Process (0):

GO Molecular Function (4): DNA binding (GO:0003677), RNA binding (GO:0003723), nucleic acid binding (GO:0003676), protein binding (GO:0005515)

GO Cellular Component (6): nucleolus (GO:0005730), cytosol (GO:0005829), Cajal body (GO:0015030), PML body (GO:0016605), nucleus (GO:0005634), cytoplasm (GO:0005737)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
nucleic acid binding	2
binding	2
cellular anatomical structure	2
nuclear lumen	1
intracellular membraneless organelle	1
cytoplasm	1
nuclear ribonucleoprotein granule	1
nuclear body	1
intracellular membrane-bounded organelle	1
intracellular anatomical structure	1

Protein interactions and networks

STRING

640 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
RDM1	RAD52	P43351	877
RDM1	DRD1	P21728	780
RDM1	TP53	P04637	570
RDM1	AMZ1	Q400G9	476
RDM1	CCDC57	Q2TAC2	460
RDM1	FASTKD3	Q14CZ7	456
RDM1	OR4D9	Q8NGE8	456
RDM1	NKAIN4	Q8IVV8	452
RDM1	OR1K1	Q8NGR3	440
RDM1	FAM111A	Q96PZ2	437
RDM1	STK31	Q9BXU1	433
RDM1	OR52W1	Q6IF63	432
RDM1	ARHGAP27	Q6ZUM4	429
RDM1	DNAJC12	Q9UKB3	425
RDM1	DMRT3	Q9NQL9	423

IntAct

24 interactions, top by confidence:

A	B	Type	Score
RDM1	MRFAP1L1	psi-mi:“MI:0915”(physical association)	0.560
MRFAP1L1	RDM1	psi-mi:“MI:0915”(physical association)	0.560
RAD52	RDM1	psi-mi:“MI:0915”(physical association)	0.560
RDM1	SCNM1	psi-mi:“MI:0915”(physical association)	0.560
CNTF	RDM1	psi-mi:“MI:0915”(physical association)	0.560
CCDC57	RDM1	psi-mi:“MI:0915”(physical association)	0.560
RDM1	PI4KB	psi-mi:“MI:0915”(physical association)	0.400
MTCH2	IPO5	psi-mi:“MI:0914”(association)	0.350
RAD52	RDM1	psi-mi:“MI:0915”(physical association)	0.000
CCDC57	RDM1	psi-mi:“MI:0915”(physical association)	0.000
SCNM1	RDM1	psi-mi:“MI:0915”(physical association)	0.000
CNTF	RDM1	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (12): RDM1 (Two-hybrid), RUVBL2 (Affinity Capture-MS), PI4KB (Affinity Capture-MS), PI4KB (Affinity Capture-MS), RUVBL2 (Affinity Capture-MS), RDM1 (Two-hybrid), RDM1 (Two-hybrid), RDM1 (Two-hybrid), RDM1 (Two-hybrid), PI4KB (Affinity Capture-MS), RDM1 (Positive Genetic), RDM1 (Affinity Capture-MS)

ESM2 similar proteins: A0JM24, A1A5R7, A2AKG8, A2CI34, D3YWQ0, F1MAB7, F6S215, O08653, O43149, O54705, O62699, P29477, P35608, P59438, P97499, Q06518, Q08DB2, Q20CR4, Q27995, Q28314, Q4R856, Q4TVR5, Q4VSN2, Q4VSN3, Q4VSN4, Q4VSN5, Q5BIW4, Q5EB20, Q5R6T6, Q5SSH7, Q5TEA3, Q5VW36, Q6NV72, Q6NXH8, Q6NXP6, Q6P996, Q6XUX0, Q6XUX1, Q6XUX2, Q6XUX3

Diamond homologs: Q4R856, Q5U3G4, Q8JFQ4, Q8NG50, Q9CQK3

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	24
Likely benign	2
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1002 predictions. Top by Δscore:

Variant	Effect	Δscore
17:35924606:T:TA	donor_gain	1.0000
17:35925509:GTTTA:G	donor_loss	1.0000
17:35925510:TTTAC:T	donor_loss	1.0000
17:35925511:TTAC:T	donor_loss	1.0000
17:35925512:TACCT:T	donor_loss	1.0000
17:35925513:A:C	donor_loss	1.0000
17:35920269:CTTT:C	acceptor_gain	0.9900
17:35922687:C:CT	acceptor_gain	0.9900
17:35924588:C:CA	donor_gain	0.9900
17:35924772:GCTGT:G	acceptor_loss	0.9900
17:35924773:C:CA	acceptor_loss	0.9900
17:35924773:C:CC	acceptor_gain	0.9900
17:35925633:CGAAC:C	acceptor_gain	0.9900
17:35925638:C:CC	acceptor_gain	0.9900
17:35925645:C:CT	acceptor_gain	0.9900
17:35925646:A:T	acceptor_gain	0.9900
17:35922676:C:CC	acceptor_gain	0.9800
17:35924769:GAAG:G	acceptor_gain	0.9800
17:35925513:A:AC	donor_gain	0.9800
17:35925514:C:CC	donor_gain	0.9800
17:35925646:A:C	acceptor_gain	0.9800
17:35930630:A:AC	donor_gain	0.9800
17:35930631:C:CC	donor_gain	0.9800
17:35920185:A:AC	donor_gain	0.9700
17:35920186:C:CC	donor_gain	0.9700
17:35922676:C:CG	acceptor_loss	0.9700
17:35924600:AGAC:A	donor_loss	0.9700
17:35924601:GA:G	donor_loss	0.9700
17:35924602:A:C	donor_loss	0.9700
17:35924603:CC:C	donor_loss	0.9700

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000299342 (17:35922420 G>A,C,T), RS1000637661 (17:35929355 G>C), RS1000678148 (17:35922946 CA>C,CAA), RS1000850853 (17:35930255 G>A,C), RS1001239274 (17:35927991 T>C), RS1001251149 (17:35919822 A>G), RS1001303792 (17:35919616 T>C,G), RS1001711705 (17:35927521 T>C), RS1001719427 (17:35921348 C>A), RS1001804946 (17:35927364 C>G,T), RS1002406403 (17:35926354 A>T), RS1002724177 (17:35920025 G>T), RS1002799606 (17:35932361 A>G), RS1003382801 (17:35930914 C>A,T), RS1003617060 (17:35925390 A>G)

Disease associations

OMIM: gene MIM:612896 | 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

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

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	decreases expression, affects cotreatment	7
trichostatin A	decreases expression	2
Phenylmercuric Acetate	affects cotreatment, decreases expression	2
bisphenol F	increases methylation	1
methylmercuric chloride	decreases expression	1
bisphenol A	increases expression	1
sodium arsenite	affects expression	1
zinc chromate	decreases expression, increases abundance	1
2,3-bis(3’-hydroxybenzyl)butyrolactone	increases expression, affects cotreatment	1
chromium hexavalent ion	decreases expression, increases abundance	1
entinostat	decreases expression	1
CPG-oligonucleotide	decreases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, decreases expression	1
dorsomorphin	affects cotreatment, decreases expression	1
MRK 003	decreases expression	1
Decitabine	affects expression	1
Vorinostat	increases expression	1
Panobinostat	affects cotreatment, decreases expression	1
Benzo(a)pyrene	affects methylation	1
Calcitriol	decreases expression, affects cotreatment	1
Cisplatin	affects expression	1
Coumestrol	increases expression, affects cotreatment	1
Estradiol	affects cotreatment, decreases expression	1
Hydrogen Peroxide	affects expression	1
N-Nitrosopyrrolidine	decreases expression	1
Silicon Dioxide	decreases expression	1
Testosterone	affects cotreatment, decreases expression	1
Tobacco Smoke Pollution	decreases expression	1
Tretinoin	decreases expression	1
Urethane	decreases expression	1

Clinical trials (associated diseases)

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