RIMBP3

gene
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Also known as KIAA1666RIMBP3.1RIMBP3A

Summary

RIMBP3 (RIMS binding protein 3, HGNC:29344) is a protein-coding gene on chromosome 22q11.21, encoding RIMS-binding protein 3A (Q9UFD9). Probable component of the manchette, a microtubule-based structure which plays a key role in sperm head morphogenesis during late stages of sperm development.

Predicted to enable benzodiazepine receptor binding activity. Predicted to be involved in fertilization and spermatid development. Predicted to be located in manchette. Predicted to be active in nucleus.

Source: NCBI Gene 85376 — RefSeq curated summary.

At a glance

  • GWAS associations: 1
  • Clinical variants (ClinVar): 208 total — 1 pathogenic
  • MANE Select transcript: NM_015672

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:29344
Approved symbolRIMBP3
NameRIMS binding protein 3
Location22q11.21
Locus typegene with protein product
StatusApproved
AliasesKIAA1666, RIMBP3.1, RIMBP3A
Ensembl geneENSG00000275793
Ensembl biotypeprotein_coding
OMIM612699
Entrez85376

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000619918

RefSeq mRNA: 1 — MANE Select: NM_015672 NM_015672

CCDS: CCDS46665

Canonical transcript exons

ENST00000619918 — 1 exons

ExonStartEnd
ENSE000037386611860581518611919

Expression profiles

Bgee: expression breadth broad, 68 present calls, max score 84.79.

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
left testisUBERON:000453384.79gold quality
testisUBERON:000047384.72gold quality
right testisUBERON:000453483.89gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047383.69gold quality
stromal cell of endometriumCL:000225562.97gold quality
granulocyteCL:000009462.70gold quality
lymph nodeUBERON:000002954.82gold quality
bone marrow cellCL:000209251.90gold quality
islet of LangerhansUBERON:000000651.61gold quality
leukocyteCL:000073850.95gold quality
bloodUBERON:000017850.29gold quality
monocyteCL:000057649.42gold quality
prefrontal cortexUBERON:000045149.02gold quality
cortical plateUBERON:000534348.99gold quality
placentaUBERON:000198748.79gold quality
spleenUBERON:000210648.43gold quality
descending thoracic aortaUBERON:000234548.17gold quality
tonsilUBERON:000237245.85gold quality
bone marrowUBERON:000237145.18gold quality
gall bladderUBERON:000211044.72silver quality
vermiform appendixUBERON:000115444.71gold quality
frontal cortexUBERON:000187044.67gold quality
right coronary arteryUBERON:000162544.58gold quality
hypothalamusUBERON:000189843.89gold quality
thoracic aortaUBERON:000151543.53gold quality
ventricular zoneUBERON:000305343.44gold quality
ascending aortaUBERON:000149642.91gold quality
pancreasUBERON:000126442.78gold quality
nucleus accumbensUBERON:000188242.55gold quality
duodenumUBERON:000211442.33silver quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-MTAB-9067yes12.31
E-ANND-3no1.46

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

26 targeting RIMBP3, 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-3617-3P99.9867.86918
HSA-MIR-450B-5P99.9271.483175
HSA-MIR-3140-3P99.8868.472069
HSA-MIR-477999.8666.501583
HSA-MIR-6727-3P99.4965.921333
HSA-MIR-1207-5P99.4969.112983
HSA-MIR-4722-3P99.3565.221099
HSA-MIR-427999.1966.702437
HSA-MIR-4763-3P99.1067.832649
HSA-MIR-939-3P98.9765.072347
HSA-MIR-4520-3P98.7566.55963
HSA-MIR-7851-3P98.7264.88980
HSA-MIR-471098.6165.961048
HSA-MIR-138-5P98.4370.491292
HSA-MIR-451898.1266.821030
HSA-MIR-1266-5P97.7166.921052
HSA-MIR-5089-3P97.5067.82758
HSA-MIR-526B-5P97.4167.991074
HSA-MIR-3187-3P97.3865.80904
HSA-MIR-342-5P97.2564.10817
HSA-MIR-4701-5P96.4568.411121
HSA-MIR-58896.4568.361127
HSA-MIR-524-3P95.1566.16109
HSA-MIR-525-3P95.1565.95109
HSA-MIR-367294.4665.67646
HSA-MIR-6864-3P94.4665.97625

Literature-anchored findings (GeneRIF, showing 1)

  • Homeodomain-interacting protein kinase HIPK4 regulates phosphorylation of manchette protein RIMBP3 during spermiogenesis. (PMID:35931115)

Cross-species orthologs

5 orthologs

OrganismSymbolGene ID
danio_rerioENSDARG00000103792
mus_musculusRimbp3ENSMUSG00000071636
rattus_norvegicusRimbp3ENSRNOG00000030452
drosophila_melanogasterRbpFBGN0262483
caenorhabditis_elegansWBGENE00006513

Paralogs (4): TSPOAP1 (ENSG00000005379), RIMBP2 (ENSG00000060709), RIMBP3C (ENSG00000183246), RIMBP3B (ENSG00000274600)

Protein

Protein identifiers

RIMS-binding protein 3AQ9UFD9 (reviewed: Q9UFD9)

Alternative names: RIMS-binding protein 3.1

All UniProt accessions (1): Q9UFD9

UniProt curated annotations — full annotation on UniProt →

Function. Probable component of the manchette, a microtubule-based structure which plays a key role in sperm head morphogenesis during late stages of sperm development.

Subunit / interactions. Interacts with LRGUK (via guanylate kinase-like domain). Interacts (via C-terminus) with HOOK1 (via coiled-coil region).

Subcellular location. Cytoplasm. Cytoskeleton.

Similarity. Belongs to the RIMBP family.

RefSeq proteins (1): NP_056487* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR001452SH3_domainDomain
IPR003961FN3_domDomain
IPR013783Ig-like_foldHomologous_superfamily
IPR036028SH3-like_dom_sfHomologous_superfamily
IPR036116FN3_sfHomologous_superfamily
IPR040325RIMBP1/2/3Family
IPR057884FN3_RIM-BP1/2/3Domain
IPR057950RIMB1/RIM3A-C-like_NDomain

Pfam: PF07653, PF25523, PF25566

UniProt features (38 total): sequence conflict 9, region of interest 6, strand 6, domain 5, compositionally biased region 5, coiled-coil region 3, turn 2, chain 1, sequence variant 1

Structure

Experimental structures (PDB)

1 structures.

PDBMethodResolution (Å)
2EGESOLUTION NMR

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q9UFD9-F158.790.18

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 42 (showing top): BENPORATH_ES_WITH_H3K27ME3, GOBP_MALE_GAMETE_GENERATION, GOBP_CELL_CELL_SIGNALING, GOBP_CELLULAR_PROCESS_INVOLVED_IN_REPRODUCTION_IN_MULTICELLULAR_ORGANISM, GARCIA_TARGETS_OF_FLI1_AND_DAX1_DN, GOBP_SYNAPTIC_SIGNALING, GOBP_DEVELOPMENTAL_PROCESS_INVOLVED_IN_REPRODUCTION, GOBP_FERTILIZATION, GOMF_SIGNALING_RECEPTOR_BINDING, GOBP_NEUROMUSCULAR_SYNAPTIC_TRANSMISSION, KOYAMA_SEMA3B_TARGETS_DN, CERIBELLI_GENES_INACTIVE_AND_BOUND_BY_NFY, FORTSCHEGGER_PHF8_TARGETS_DN, GOCC_MANCHETTE, ZWANG_TRANSIENTLY_UP_BY_2ND_EGF_PULSE_ONLY

GO Biological Process (4): spermatid development (GO:0007286), fertilization (GO:0009566), spermatogenesis (GO:0007283), cell differentiation (GO:0030154)

GO Molecular Function (2): benzodiazepine receptor binding (GO:0030156), protein binding (GO:0005515)

GO Cellular Component (4): nucleus (GO:0005634), cytoskeleton (GO:0005856), manchette (GO:0002177), cytoplasm (GO:0005737)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cellular anatomical structure2
germ cell development1
spermatid differentiation1
sexual reproduction1
reproductive process1
developmental process involved in reproduction1
male gamete generation1
cellular developmental process1
signaling receptor binding1
binding1
intracellular membrane-bounded organelle1
intracellular membraneless organelle1
microtubule cytoskeleton1
intracellular anatomical structure1

Protein interactions and networks

STRING

764 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
RIMBP3HOOK1Q9UJC3870
RIMBP3KIF3BO15066743
RIMBP3HOOK2Q96ED9687
RIMBP3RIMS2Q9UQ26620
RIMBP3TMEM191BP0C7N4583
RIMBP3MORN3Q6PF18575
RIMBP3FN1P02751566
RIMBP3C20orf173Q96LM9519
RIMBP3CCDC54Q8NEL0513
RIMBP3SRCP12931494
RIMBP3RIMS1Q86UR5481
RIMBP3MVPQ14764476
RIMBP3C22orf23Q9BZE7471
RIMBP3LRGUKQ96M69454
RIMBP3TMCO5AQ8N6Q1450

IntAct

111 interactions, top by confidence:

ABTypeScore
POLR1CRIMBP3psi-mi:“MI:0915”(physical association)0.720
RIMBP3POLR1Cpsi-mi:“MI:0915”(physical association)0.720
RIMBP3PRKAB2psi-mi:“MI:0915”(physical association)0.670
RIMBP3NOXA1psi-mi:“MI:0915”(physical association)0.670
PRKAB2RIMBP3psi-mi:“MI:0915”(physical association)0.670
NOXA1RIMBP3psi-mi:“MI:0915”(physical association)0.670
RIMBP3TRAF3IP2psi-mi:“MI:0915”(physical association)0.560
AQP1RIMBP3psi-mi:“MI:0915”(physical association)0.560
RIMBP3CREB5psi-mi:“MI:0915”(physical association)0.560
RIMBP3TLE5psi-mi:“MI:0915”(physical association)0.560
PRKAA1RIMBP3psi-mi:“MI:0915”(physical association)0.560
DTX2RIMBP3psi-mi:“MI:0915”(physical association)0.560
RIMBP3CTBP2psi-mi:“MI:0915”(physical association)0.560
CATSPER1RIMBP3psi-mi:“MI:0915”(physical association)0.560
ZNF488RIMBP3psi-mi:“MI:0915”(physical association)0.560
DGCR6LRIMBP3psi-mi:“MI:0915”(physical association)0.560
RIMBP3FANCLpsi-mi:“MI:0915”(physical association)0.560
RIMBP3PPIL1psi-mi:“MI:0915”(physical association)0.560
TRAF3IP2RIMBP3psi-mi:“MI:0915”(physical association)0.560
RIMBP3AQP1psi-mi:“MI:0915”(physical association)0.560
CREB5RIMBP3psi-mi:“MI:0915”(physical association)0.560

BioGRID (26): RIMBP3 (Two-hybrid), RIMBP3 (Two-hybrid), RIMBP3 (Two-hybrid), RIMBP3 (Two-hybrid), RIMBP3 (Two-hybrid), RIMBP3 (Two-hybrid), RIMBP3 (Two-hybrid), RIMBP3 (Two-hybrid), RIMBP3 (Two-hybrid), RIMBP3 (Two-hybrid), RIMBP3 (Two-hybrid), RIMBP3 (Two-hybrid), DTX2 (Two-hybrid), CATSPER1 (Two-hybrid), ZNF488 (Two-hybrid)

ESM2 similar proteins: A0A140LIT1, A0A1B0GVG4, A0JNH6, A1A5D9, A6NC98, A6NGB0, A6NJZ7, A6NNM3, F6XLV1, O15049, O54887, P0C7N4, P58660, P60531, Q0D2H9, Q0P5D1, Q2KJ21, Q2TAC2, Q3LUD3, Q3T1I3, Q3TMW1, Q3V0F0, Q4QRL3, Q5JTB6, Q5RD60, Q66HR5, Q6NSJ2, Q6PHN1, Q6QZQ4, Q80VM7, Q8BP01, Q8C7U1, Q8CB62, Q8CGU1, Q8CHW5, Q8K2I2, Q8N137, Q8N283, Q8N6Y0, Q8R370

Diamond homologs: A6NJZ7, A6NNM3, O95153, Q3V0F0, Q80U40, Q9JIR1, Q9UFD9, O15034, Q7TNF8, Q8QFX1, Q9JIR0, E2RP94, M0R4F8, Q6XJU9, Q6XZF7, A0A0K3AV08, A1CEK6, A1DFN5, A2QW93, Q0CJU8, Q15811, Q4WHP5, Q557J6, Q5BBL4, Q96B97

SIGNOR signaling

3 interactions.

AEffectBMechanism
RIMBP3“down-regulates activity”RIMS1binding
RIMBP3“down-regulates activity”RIMS2binding
RIMBP3“down-regulates activity”RIMS3binding

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic1
Likely pathogenic0
Uncertain significance179
Likely benign28
Benign0

Top pathogenic / likely-pathogenic (1)

Variant IDHGVSClassification
1077190Single allelePathogenic

SpliceAI

24 predictions. Top by Δscore:

VariantEffectΔscore
22:18605993:A:Cacceptor_gain0.6000
22:18611872:GCATA:Gdonor_loss0.4200
22:18611873:CATA:Cdonor_loss0.4200
22:18611874:ATACC:Adonor_loss0.4200
22:18611875:TACCT:Tdonor_loss0.4200
22:18611876:ACCT:Adonor_loss0.4200
22:18611877:CC:Cdonor_loss0.4200
22:18605998:G:GCacceptor_gain0.4100
22:18611878:C:Adonor_loss0.3900
22:18605988:C:Aacceptor_gain0.3600
22:18605990:C:Aacceptor_gain0.3600
22:18611871:GGCAT:Gdonor_loss0.3500
22:18606078:TCG:Tacceptor_gain0.3400
22:18606079:CGC:Cacceptor_gain0.3400
22:18606001:G:Cacceptor_gain0.3200
22:18611879:T:Adonor_loss0.3100
22:18605977:T:Aacceptor_gain0.3000
22:18605989:G:Aacceptor_gain0.2700
22:18611874:A:Tdonor_gain0.2500
22:18606001:G:GCacceptor_gain0.2400
22:18605979:C:CCacceptor_gain0.2200
22:18605992:C:Aacceptor_gain0.2200
22:18606193:T:TGacceptor_gain0.2100
22:18611870:GGGC:Gdonor_loss0.2000

AlphaMissense

10547 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
22:18608116:A:GW1107R0.988
22:18608116:A:TW1107R0.988
22:18608056:C:GA1127P0.984
22:18608114:C:AW1107C0.975
22:18608114:C:GW1107C0.975
22:18608201:G:CF1078L0.975
22:18608201:G:TF1078L0.975
22:18608203:A:GF1078L0.975
22:18611031:A:GL135P0.975
22:18608807:G:CF876L0.974
22:18608807:G:TF876L0.974
22:18608809:A:GF876L0.974
22:18611025:C:GR137P0.973
22:18611041:C:GA132P0.971
22:18611019:A:GL139P0.969
22:18611118:A:GL106P0.968
22:18608059:A:GY1126H0.963
22:18608398:A:GW1013R0.963
22:18608398:A:TW1013R0.963
22:18608121:A:TV1105D0.961
22:18610838:G:CF199L0.959
22:18610838:G:TF199L0.959
22:18610840:A:GF199L0.959
22:18608052:A:TV1128E0.954
22:18608059:A:CY1126D0.952
22:18608202:A:GF1078S0.951
22:18611105:C:AK110N0.951
22:18611105:C:GK110N0.951
22:18607940:T:AR1165S0.950
22:18607940:T:GR1165S0.950

dbSNP variants (sampled 300 via entrez): RS1001858495 (22:18606912 C>G,T), RS1003534567 (22:18612228 G>A,T), RS1003588524 (22:18610018 A>G,T), RS1006809781 (22:18609196 C>T), RS1007168093 (22:18609820 G>A), RS1010665331 (22:18607808 G>C), RS1011049861 (22:18607044 T>A,C), RS1012310369 (22:18612900 C>T), RS1017302353 (22:18609253 G>A), RS1020801560 (22:18607051 CAG>C), RS1021084271 (22:18607847 G>A,C), RS1022892017 (22:18613128 C>T), RS1026252754 (22:18609433 G>C), RS1026287169 (22:18609977 G>A), RS1029489532 (22:18608114 C>G,T)

Disease associations

OMIM: gene MIM:612699 | disease phenotypes: MIM:188400

GenCC curated gene-disease

Mondo (1): DiGeorge syndrome (MONDO:0008564)

Orphanet (1): 22q11.2 deletion syndrome (Orphanet:567)

HPO phenotypes

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

GWAS associations

1 associations (top):

StudyTraitp-value
GCST001725_108Inflammatory bowel disease1.000000e-16

MeSH disease descriptors (1)

DescriptorNameTree numbers
D004062DiGeorge SyndromeC05.660.207.103.500; C14.240.400.021.500; C14.280.400.044.500; C15.604.451.249.500; C16.131.077.019.500; C16.131.240.400.021.500; C16.131.260.019.500; C16.131.482.249.500; C16.131.621.207.103.500; C16.320.180.019.500; C19.642.482.500.500

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

26 total (human), top 26 by PubMed support.

ChemicalActions (top 5)PubMed papers
afuresertibincreases expression1
bisphenol Aaffects cotreatment, increases expression1
titanium dioxidedecreases expression1
tris(1,3-dichloro-2-propyl)phosphatedecreases expression1
cobaltous chlorideincreases expression1
perfluorooctanoic acidincreases expression1
tobacco tardecreases expression, decreases reaction1
diallyl disulfidedecreases expression, decreases reaction1
ferrous chloridedecreases expression1
coumarinincreases phosphorylation1
allyl sulfidedecreases expression, decreases reaction1
S-(1,2-dichlorovinyl)cysteineaffects response to substance, increases expression, affects cotreatment, decreases expression1
erucylphospho-N,N,N-trimethylpropylammoniumincreases expression1
abrinedecreases expression1
Resveratrolaffects cotreatment, decreases expression1
Dexamethasoneaffects cotreatment, increases expression1
Doxorubicindecreases expression1
Estradiolincreases expression, affects cotreatment1
Indomethacinincreases expression, affects cotreatment1
Lipopolysaccharidesaffects response to substance, increases expression, affects cotreatment, decreases expression1
Plant Extractsaffects cotreatment, decreases expression1
Smokedecreases expression1
Valproic Acidincreases methylation1
1-Methyl-3-isobutylxanthineincreases expression, affects cotreatment1
Copper Sulfatedecreases expression1
Magnetite Nanoparticlesdecreases expression1

Clinical trials (associated diseases)

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

TrialPhaseStatusTitle
NCT00395538PHASE3TERMINATEDEffects of PTH Replacement on Bone in Hypoparathyroidism
NCT00576407PHASE2COMPLETEDThymus Transplantation in DiGeorge Syndrome #668
NCT00576836PHASE2COMPLETEDThymus Transplantation Dose in DiGeorge #932
NCT01821781PHASE2ACTIVE_NOT_RECRUITINGImmune Disorder HSCT Protocol
NCT05149898PHASE2COMPLETEDOpen-Label Study of ZYN002 Administered as a Transdermal Gel to Children and Adolescents With 22q11.2 Deletion Syndrome (INSPIRE)
NCT07284641PHASE2RECRUITINGHematopoietic Stem Cell Transplantation (HSCT) for Common Variable Immunodeficiency (CVID) and Other Autoimmune Manifestations of Primary Immune Regulatory Disorders (PIRD)
NCT00566488PHASE1COMPLETEDParathyroid and Thymus Transplantation in DiGeorge #931
NCT00579709PHASE1COMPLETEDThymus Transplantation With Immunosuppression
NCT00849888PHASE1TERMINATEDSerum-Free Thymus Transplantation in DiGeorge Anomaly
NCT02895906PHASE1COMPLETEDSafety and Efficacy Study of NFC-1 in Subjects Aged 12-17 Years With 22q11.2DS & Associated Neuropsychiatric Conditions
NCT00579527PHASE1/PHASE2COMPLETEDPhase I/II Thymus Transplantation With Immunosuppression #950
NCT00004351Not specifiedCOMPLETEDStudy of Phenotype and Genotype Correlations in Patients With Contiguous Gene Deletion Syndromes
NCT00005102Not specifiedUNKNOWNImmunologic Evaluation in Patients With DiGeorge Syndrome or Velocardiofacial Syndrome
NCT00105274Not specifiedCOMPLETEDVelocardiofacial (VCFS; 22q11.2; DiGeorge) Syndrome Study
NCT00278005Not specifiedTERMINATEDInfection in DiGeorge Following CHD Surgery
NCT00556530Not specifiedRECRUITINGExamining Genetic Factors That Affect the Severity of 22q11.2 Deletion Syndrome
NCT00916955Not specifiedCOMPLETEDGenetic Modifiers for 22q11.2 Syndrome
NCT01220531Not specifiedCOMPLETEDThymus Transplantation Safety-Efficacy
NCT01781923Not specifiedCOMPLETEDCognitive Remediation in 22q11DS
NCT02381457Not specifiedCOMPLETEDSNP-based Microdeletion and Aneuploidy RegisTry (SMART)
NCT02430584Not specifiedUNKNOWNWhole Blood Specimen Collection From Pregnant Subjects
NCT02460328Not specifiedCOMPLETEDResolution of Primary Immune Defect in 22q11.2 Deletion Syndrome
NCT02787486Not specifiedCOMPLETEDExpanded Noninvasive Genomic Medical Assessment: The Enigma Study
NCT03284060Not specifiedTERMINATEDSocial Cognition Training and Cognitive Remediation
NCT04141540Not specifiedCOMPLETEDMolecular Variants Associated With Schizophrenia: Differential Analysis of Monozygotic Twins With Variable Phenotypic 22q11
NCT04373226Not specifiedTERMINATEDArithmetic Abilities in Children With 22q11.2DS
NCT04639388Not specifiedRECRUITINGUnderstanding of Psychotic Disorders in Children With 22q11.2DS
NCT04639960Not specifiedTERMINATEDNeuroprotective Effects of Risperdal on Brain and Cognition in 22q11 Deletion Syndrome
NCT04647500Not specifiedCOMPLETEDEffects of Methylphenidate on Brain and Cognition in 22q11 Deletion Syndrome
NCT05924347Not specifiedRECRUITINGEarly Scoliotic Changes in Children at Increased Risk for Scoliosis Development
NCT07493096Not specifiedRECRUITINGIntensive Multimodal Neurorehabilitation Targeting Neuroplasticity in Pediatric Neurodevelopmental and Chromosomal Disorders
  • Disease cohort memberships (association, not causation — diseases whose associated-gene cohort lists this gene; a subset are also under Associated diseases): DiGeorge syndrome