RHNO1

gene
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Also known as HKMT1188MGC13204RHINO

Summary

RHNO1 (RAD9-HUS1-RAD1 interacting nuclear orphan 1, HGNC:28206) is a protein-coding gene on chromosome 12p13.33, encoding RAD9, HUS1, RAD1-interacting nuclear orphan protein 1 (Q9BSD3). Involved in microhomology-mediated end-joining (MMEJ) DNA repair by promoting recruitment of polymerase theta (POLQ) to DNA damage sites during mitosis.

Enables chromatin-protein adaptor activity. Involved in several processes, including DNA repair; cellular response to radiation; and regulation of cell cycle process. Located in chromosome and nucleus. Is active in chromatin and site of double-strand break.

Source: NCBI Gene 83695 — RefSeq curated summary.

At a glance

  • GWAS associations: 4
  • Clinical variants (ClinVar): 11 total
  • MANE Select transcript: NM_001252499

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:28206
Approved symbolRHNO1
NameRAD9-HUS1-RAD1 interacting nuclear orphan 1
Location12p13.33
Locus typegene with protein product
StatusApproved
AliasesHKMT1188, MGC13204, RHINO
Ensembl geneENSG00000171792
Ensembl biotypeprotein_coding
OMIM614085
Entrez83695

Gene structure

Transcript identifiers

Ensembl transcripts: 12 — 8 protein_coding, 2 protein_coding_CDS_not_defined, 1 nonsense_mediated_decay, 1 TEC

ENST00000366285, ENST00000461997, ENST00000464682, ENST00000489288, ENST00000535978, ENST00000536063, ENST00000538636, ENST00000538700, ENST00000618250, ENST00000623153, ENST00000949626, ENST00000949627

RefSeq mRNA: 4 — MANE Select: NM_001252499 NM_001252499, NM_001252500, NM_001257097, NM_001257098

CCDS: CCDS58199, CCDS8518

Canonical transcript exons

ENST00000489288 — 3 exons

ExonStartEnd
ENSE0000203939028852832885534
ENSE0000229584828879112889524
ENSE0000360504028772232877282

Expression profiles

Bgee: expression breadth ubiquitous, 235 present calls, max score 96.32.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.0615 / max 4.2690, expressed in 13 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter IDTPM avgSamples expressed
12345449.59061817
1234530.061513

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
ventricular zoneUBERON:000305396.32gold quality
ganglionic eminenceUBERON:000402395.34gold quality
cortical plateUBERON:000534394.92gold quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099193.16gold quality
oviduct epitheliumUBERON:000480490.50gold quality
bone marrow cellCL:000209288.56gold quality
islet of LangerhansUBERON:000000686.37gold quality
rectumUBERON:000105285.89gold quality
granulocyteCL:000009485.82gold quality
stromal cell of endometriumCL:000225585.58gold quality
prefrontal cortexUBERON:000045185.58gold quality
smooth muscle tissueUBERON:000113585.58gold quality
olfactory segment of nasal mucosaUBERON:000538685.29gold quality
bone marrowUBERON:000237185.09gold quality
vermiform appendixUBERON:000115485.08gold quality
esophagus mucosaUBERON:000246985.03gold quality
lymph nodeUBERON:000002984.47gold quality
gall bladderUBERON:000211084.40gold quality
fallopian tubeUBERON:000388983.79gold quality
lower esophagus mucosaUBERON:003583483.77gold quality
adrenal tissueUBERON:001830383.62gold quality
ileal mucosaUBERON:000033183.51gold quality
skin of abdomenUBERON:000141683.45gold quality
skin of legUBERON:000151183.31gold quality
adenohypophysisUBERON:000219683.25gold quality
leukocyteCL:000073883.22gold quality
prostate glandUBERON:000236782.97gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047382.92gold quality
anterior cingulate cortexUBERON:000983582.80gold quality
caudate nucleusUBERON:000187382.77gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 1.

ExperimentMarker?Max mean expression
E-MTAB-6142no243.17
E-ANND-3no0.00

Regulation

Is transcription factor: no

Literature-anchored findings (GeneRIF, showing 8)

  • Identified C12orf32 to be significantly up-regulated in the great majority of clinical breast cancer specimens. (PMID:20811708)
  • We suggest that RHINO functions together with the 9-1-1 complex and TopBP1 to fully activate ATR (ataxia telangiectasia and Rad3-related. (PMID:21659603)
  • Germline variation in the RHINO gene is unlikely to influence inherited susceptibility to breast cancer. (PMID:24562772)
  • Knockdown of RHINO in human cells partially abrogated ATR-Chk1 kinase signaling following UV irradiation but did not impact the loading of Rad9-Hus1-Rad1 complex on chromatin or the association of Rad9-Hus1-Rad1 complex with TopBP1. (PMID:25602520)
  • Co-regulation and function of FOXM1/RHNO1 bidirectional genes in cancer. (PMID:33890574)
  • RHNO1 disruption inhibits cell proliferation and induces mitochondrial apoptosis via PI3K/Akt pathway in hepatocellular carcinoma. (PMID:37364391)
  • RHINO directs MMEJ to repair DNA breaks in mitosis. (PMID:37440612)
  • Structural basis for intra- and intermolecular interactions on RAD9 subunit of 9-1-1 checkpoint clamp implies functional 9-1-1 regulation by RHINO. (PMID:38354779)

Cross-species orthologs

3 orthologs

OrganismSymbolGene ID
mus_musculusRhno1ENSMUSG00000048668
rattus_norvegicusRhno1ENSRNOG00000028517
rattus_norvegicusRhno1-ps2ENSRNOG00000067361

Protein

Protein identifiers

RAD9, HUS1, RAD1-interacting nuclear orphan protein 1Q9BSD3 (reviewed: Q9BSD3)

Alternative names: RAD9, RAD1, HUS1-interacting nuclear orphan protein

All UniProt accessions (5): Q9BSD3, F5H0U1, F5H580, F5H795, F5H7S2

UniProt curated annotations — full annotation on UniProt →

Function. Involved in microhomology-mediated end-joining (MMEJ) DNA repair by promoting recruitment of polymerase theta (POLQ) to DNA damage sites during mitosis. MMEJ is an alternative non-homologous end-joining (NHEJ) machinery that takes place during mitosis to repair double-strand breaks in DNA that originate in S-phase. Accumulates in M-phase; following phosphorylation by PLK1, interacts with POLQ, enabling its recruitment to double-strand breaks for subsequent repair. Also involved in the DNA damage response (DDR) signaling in response to genotoxic stresses such as ionizing radiation (IR) during the S phase. Recruited to sites of DNA damage through interaction with the 9-1-1 cell-cycle checkpoint response complex and TOPBP1 in a ATR-dependent manner. Required for the progression of the G1 to S phase transition. Plays a role in the stimulation of CHEK1 phosphorylation.

Subunit / interactions. Interacts (when phosphorylated by PLK1) with POLQ; promoting POLQ recruitment to DNA damage sites. Interacts with RAD1; interaction is direct and promotes association with the 9-1-1 (RAD9-RAD1-HUS1) complex. Interacts with RAD18. Interacts with TOPBP1. Interacts with UBE2N.

Subcellular location. Nucleus. Chromosome.

Tissue specificity. Weakly expressed in testis, prostate, ovary, thymus and small intestine. Expressed strongly in breast cancer cells.

Post-translational modifications. Phosphorylated at Ser-51 by PLK1, promoting interaction with polymerase theta (POLQ). Ubiquitinated and degraded by the APC/C complex upon mitotic exit.

Domain organisation. The RAD1-binding motif mediates interaction with RAD1.

Induction. Up-regulated in breast cancer cells.

Isoforms (2)

UniProt IDNamesCanonical?
Q9BSD3-11yes
Q9BSD3-22

RefSeq proteins (4): NP_001239428, NP_001239429, NP_001244026, NP_001244027 (=MANE)

Domains & families (InterPro)

IDNameType
IPR029293RHNO1Family

Pfam: PF15319

UniProt features (18 total): mutagenesis site 8, short sequence motif 3, region of interest 2, compositionally biased region 2, chain 1, modified residue 1, splice variant 1

Structure

Experimental structures (PDB)

2 structures.

PDBMethodResolution (Å)
6J8YX-RAY DIFFRACTION2.4
8WU8X-RAY DIFFRACTION2.81

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q9BSD3-F165.660.07

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): 51

Mutagenesis-validated functional residues (8):

PositionPhenotype
51–52in rhino-plk1s/t(7a) mutant; abolished phosphorylation leading to decreased interaction with polq; when associated with
51abolished phosphorylation by plk1, leading to decreased interaction with polq.
55–61inhibits binding to the 9-1-1 complex. does not inhibit interaction with topbp1. inhibits localizion to sites of dna dam
125–132abolished degradation following mitosis; when associated with 174-missing-178.
141in rhino-plk1s/t(7a) mutant; abolished phosphorylation leading to decreased interaction with polq; when associated with
162–164in rhino-plk1s/t(7a) mutant; abolished phosphorylation leading to decreased interaction with polq; when associated with
174–178abolished degradation following mitosis; when associated with 125-missing-132.
178in rhino-plk1s/t(7a) mutant; abolished phosphorylation leading to decreased interaction with polq; when associated with

Function

Pathways and Gene Ontology

Reactome pathways

6 pathways

IDPathway
R-HSA-5685938HDR through Single Strand Annealing (SSA)
R-HSA-5693607Processing of DNA double-strand break ends
R-HSA-5693616Presynaptic phase of homologous DNA pairing and strand exchange
R-HSA-6804756Regulation of TP53 Activity through Phosphorylation
R-HSA-69473G2/M DNA damage checkpoint
R-HSA-9709570Impaired BRCA2 binding to RAD51

MSigDB gene sets: 124 (showing top): GOBP_RESPONSE_TO_IONIZING_RADIATION, GOBP_CELLULAR_RESPONSE_TO_UV, REACTOME_G2_M_DNA_DAMAGE_CHECKPOINT, GOBP_CELLULAR_RESPONSE_TO_LIGHT_STIMULUS, GOBP_CELL_CYCLE_PHASE_TRANSITION, PATIL_LIVER_CANCER, CREIGHTON_ENDOCRINE_THERAPY_RESISTANCE_1, GOBP_NEGATIVE_REGULATION_OF_CELL_CYCLE_PROCESS, GOBP_NEGATIVE_REGULATION_OF_CELL_CYCLE, GOBP_PROTEIN_LOCALIZATION_TO_CHROMOSOME, GOBP_REGULATION_OF_CELL_CYCLE, GOBP_POSITIVE_REGULATION_OF_CELL_CYCLE_PROCESS, GOBP_RESPONSE_TO_UV, GOBP_DNA_DAMAGE_RESPONSE, GOBP_RESPONSE_TO_RADIATION

GO Biological Process (10): DNA damage checkpoint signaling (GO:0000077), recombinational repair (GO:0000725), cellular response to UV (GO:0034644), positive regulation of G0 to G1 transition (GO:0070318), cellular response to ionizing radiation (GO:0071479), double-strand break repair via alternative nonhomologous end joining (GO:0097681), protein localization to site of double-strand break (GO:1990166), DNA repair (GO:0006281), chromatin organization (GO:0006325), DNA damage response (GO:0006974)

GO Molecular Function (2): chromatin-protein adaptor activity (GO:0140463), protein binding (GO:0005515)

GO Cellular Component (5): chromatin (GO:0000785), nucleus (GO:0005634), nucleoplasm (GO:0005654), chromosome (GO:0005694), site of double-strand break (GO:0035861)

Reactome top-level categories

Rollup of top-5 pathways:

CategoryPathways
HDR through Homologous Recombination (HRR) or Single Strand Annealing (SSA)2
Homologous DNA Pairing and Strand Exchange1
Regulation of TP53 Activity1
G2/M Checkpoints1
Defective homologous recombination repair (HRR) due to BRCA2 loss of function1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cellular anatomical structure2
DNA integrity checkpoint signaling1
signal transduction in response to DNA damage1
DNA repair1
DNA recombination1
response to UV1
cellular response to light stimulus1
G0 to G1 transition1
regulation of G0 to G1 transition1
positive regulation of cell cycle process1
response to ionizing radiation1
cellular response to radiation1
double-strand break repair via nonhomologous end joining1
protein localization to chromosome1
DNA metabolic process1
DNA damage response1
cellular component organization1
cellular response to stress1
chromatin binding1
chromatin organization1
protein-macromolecule adaptor activity1
binding1
chromosome1
intracellular membrane-bounded organelle1
nuclear lumen1
intracellular membraneless organelle1
site of DNA damage1

Protein interactions and networks

STRING

762 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
RHNO1TOPBP1Q92547712
RHNO1HUS1O60921528
RHNO1ATOSBQ7L5A3506
RHNO1TEX52A6NCN8479
RHNO1C22orf39Q6P5X5466
RHNO1RAD9AQ99638463
RHNO1TTLL5Q6EMB2462
RHNO1PWP1Q13610461
RHNO1DCAF11Q8TEB1456
RHNO1CRYL1Q9Y2S2448
RHNO1ACSL5Q9ULC5443
RHNO1COG1Q8WTW3438
RHNO1ATP8A2Q9NTI2437
RHNO1COLEC12Q5KU26434
RHNO1AP4M1O00189433

IntAct

37 interactions, top by confidence:

ABTypeScore
TFIP11RHNO1psi-mi:“MI:0915”(physical association)0.760
RHNO1TFIP11psi-mi:“MI:0915”(physical association)0.760
RHNO1psi-mi:“MI:0915”(physical association)0.560
RHNO1KRTAP10-9psi-mi:“MI:0915”(physical association)0.560
RHNO1GOLGA2psi-mi:“MI:0915”(physical association)0.560
LZTS2RHNO1psi-mi:“MI:0915”(physical association)0.560
RHNO1psi-mi:“MI:0915”(physical association)0.560
KRTAP10-9RHNO1psi-mi:“MI:0915”(physical association)0.560
GOLGA2RHNO1psi-mi:“MI:0915”(physical association)0.560
BANPRHNO1psi-mi:“MI:0915”(physical association)0.560
CYSRT1RHNO1psi-mi:“MI:0915”(physical association)0.560
KRTAP10-8RHNO1psi-mi:“MI:0915”(physical association)0.560
RHNO1BACE2psi-mi:“MI:0915”(physical association)0.560
RHNO1LRRK2psi-mi:“MI:0407”(direct interaction)0.440
RHNO1CCNDBP1psi-mi:“MI:0915”(physical association)0.370
CUL3PXDNLpsi-mi:“MI:0914”(association)0.350
RHNO1RAD1psi-mi:“MI:0914”(association)0.350
TP53BP1PSMD14psi-mi:“MI:2364”(proximity)0.270
BRCA1SMCHD1psi-mi:“MI:2364”(proximity)0.270

BioGRID (44): RHNO1 (Two-hybrid), RHNO1 (Two-hybrid), LZTS2 (Two-hybrid), KRTAP10-9 (Two-hybrid), KRTAP10-3 (Two-hybrid), TOPBP1 (Affinity Capture-Western), RAD9A (Affinity Capture-Western), RAD18 (Affinity Capture-Western), UBE2N (Affinity Capture-Western), HUS1 (Affinity Capture-MS), RAD1 (Affinity Capture-MS), UBE2N (Affinity Capture-MS), RAD18 (Affinity Capture-MS), TOPBP1 (Affinity Capture-MS), RAD9A (Affinity Capture-MS)

ESM2 similar proteins: A0A087WXM9, A0A2K1JJ00, A0JM83, A4IGL8, E1BC15, E9Q5F9, O14513, O35923, O60673, O88491, P46013, P97929, Q14B71, Q28DZ0, Q29RT4, Q3MHH3, Q3TNU4, Q3ZBP0, Q4QY64, Q4V7J0, Q5DTT3, Q5E9A0, Q5F2C3, Q5RD08, Q5VWN6, Q5VYV7, Q61493, Q69YH5, Q6NS59, Q703I1, Q80U59, Q86XD8, Q8IXS0, Q8IYL3, Q8L7I1, Q8N7Z5, Q8NFU7, Q8TEP8, Q92628, Q96BU1

Diamond homologs: Q1LZE2, Q6AY26, Q8K3A4, Q9BSD3

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance1
Likely benign2
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

542 predictions. Top by Δscore:

VariantEffectΔscore
12:2877278:GGCTG:Gdonor_gain1.0000
12:2877279:GCTGG:Gdonor_gain1.0000
12:2877282:GGT:Gdonor_loss1.0000
12:2877283:GTAAG:Gdonor_loss1.0000
12:2877284:T:Adonor_loss1.0000
12:2877279:GCTG:Gdonor_gain0.9900
12:2877283:G:GGdonor_gain0.9900
12:2876915:CTCA:Cdonor_loss0.9800
12:2876916:TCA:Tdonor_loss0.9800
12:2876917:CACCT:Cdonor_loss0.9800
12:2876918:A:Cdonor_loss0.9800
12:2877313:G:GTdonor_gain0.9800
12:2877313:G:Tdonor_gain0.9800
12:2876914:GCTCA:Gdonor_loss0.9700
12:2887909:A:Gacceptor_gain0.9700
12:2876790:C:Adonor_gain0.9600
12:2876839:C:CAdonor_gain0.9600
12:2876847:T:TAdonor_gain0.9600
12:2876921:T:TAdonor_gain0.9600
12:2887043:A:Gdonor_gain0.9600
12:2887032:G:GTdonor_gain0.9500
12:2887047:A:AGdonor_gain0.9400
12:2887906:TTAA:Tacceptor_loss0.9400
12:2887907:TAA:Tacceptor_loss0.9400
12:2887908:AAGGT:Aacceptor_loss0.9400
12:2876789:T:TAdonor_gain0.9300
12:2877316:G:GTdonor_gain0.9300
12:2877280:CTG:Cdonor_gain0.9200
12:2876769:TGC:Tdonor_gain0.9100
12:2876918:A:ACdonor_gain0.9100

AlphaMissense

1542 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
12:2888379:T:AW213R0.993
12:2888379:T:CW213R0.993
12:2888381:G:CW213C0.987
12:2888381:G:TW213C0.987
12:2888384:G:CR214S0.975
12:2888384:G:TR214S0.975
12:2885418:T:CF18L0.970
12:2885420:C:AF18L0.970
12:2885420:C:GF18L0.970
12:2885532:T:AW56R0.964
12:2885532:T:CW56R0.964
12:2888389:G:CR216P0.963
12:2888380:G:CW213S0.961
12:2888410:T:CL223P0.960
12:2887923:T:CF61L0.954
12:2887925:T:AF61L0.954
12:2887925:T:GF61L0.954
12:2885534:G:CW56C0.949
12:2885534:G:TW56C0.949
12:2888383:G:CR214T0.949
12:2888028:T:CF96L0.948
12:2888030:T:AF96L0.948
12:2888030:T:GF96L0.948
12:2888362:A:CY207S0.945
12:2888361:T:CY207H0.944
12:2888013:T:CF91L0.943
12:2888015:T:AF91L0.943
12:2888015:T:GF91L0.943
12:2888343:G:CD201H0.933
12:2888428:T:CL229P0.933

dbSNP variants (sampled 300 via entrez): RS1000153119 (12:2882759 T>C), RS1000266917 (12:2877271 C>A,T), RS1000319560 (12:2877170 G>C,T), RS1000484363 (12:2883084 A>C), RS1000851602 (12:2884867 A>C), RS1001153368 (12:2878167 G>A,T), RS1001252557 (12:2877466 C>G), RS1001365770 (12:2884088 T>A), RS1001468904 (12:2888557 T>C), RS1001562886 (12:2881398 C>T), RS1001584578 (12:2882627 C>T), RS1001658277 (12:2882367 A>G,T), RS1001714323 (12:2876503 G>A), RS1002205126 (12:2878806 T>C), RS1002228588 (12:2876814 G>A)

Disease associations

OMIM: gene MIM:614085 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

4 associations (top):

StudyTraitp-value
GCST90002390_45Mean corpuscular hemoglobin5.000000e-13
GCST90002392_366Mean corpuscular volume1.000000e-15
GCST90002396_512Mean reticulocyte volume1.000000e-11
GCST90002397_410Mean spheric corpuscular volume1.000000e-17

EFO canonical traits (2, from GWAS)

EFO IDTrait name
EFO:0004527mean corpuscular hemoglobin
EFO:0010701mean reticulocyte volume

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
Valproic Acidaffects cotreatment, decreases expression5
trichostatin Aaffects cotreatment, decreases expression, affects expression4
sodium arsenitedecreases expression, increases abundance, increases expression3
Phenylmercuric Acetateaffects cotreatment, decreases expression2
Particulate Matterdecreases expression, decreases reaction, increases abundance2
methylmercuric chloridedecreases expression1
beta-lapachoneincreases expression1
2,3-bis(3’-hydroxybenzyl)butyrolactoneaffects cotreatment, increases expression1
diallyl trisulfidedecreases expression1
di-n-butylphosphoric acidaffects expression1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, decreases expression1
erucylphospho-N,N,N-trimethylpropylammoniumdecreases expression1
2-methyl-2H-pyrazole-3-carboxylic acid (2-methyl-4-o-tolylazophenyl)amidedecreases expression, decreases reaction1
dorsomorphindecreases expression, affects cotreatment1
jinfukangincreases expression, affects cotreatment1
NSC 689534affects binding, decreases expression1
Resveratrolincreases expression, affects cotreatment1
Sunitinibdecreases expression1
Leflunomidedecreases expression1
Air Pollutantsdecreases expression, increases abundance1
Arsenicdecreases expression, increases abundance1
Vehicle Emissionsdecreases expression, decreases reaction1
Azathioprinedecreases expression1
Benzo(a)pyreneincreases expression1
Cisplatinaffects cotreatment, increases expression1
Copperaffects binding, decreases expression1
Coumestrolaffects cotreatment, increases expression1
Doxorubicindecreases expression1
Estradiolincreases expression1
Hydrogen Peroxideaffects cotreatment, increases 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.