RNF212B

gene
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Summary

RNF212B (ring finger protein 212B, HGNC:20438) is a protein-coding gene on chromosome 14q11.2, encoding E3 ubiquitin-protein ligase RNF212B (A8MTL3). Ubiquitin E3 ligase that acts as a crucial factor for crossing-over (CO) formation during meiosis.

Predicted to enable SUMO transferase activity and ubiquitin protein ligase activity. Predicted to be involved in chiasma assembly and protein ubiquitination. Predicted to be located in chromosome. Predicted to be active in synaptonemal complex.

Source: NCBI Gene 100507650 — RefSeq curated summary.

At a glance

  • Gene–disease (curated): infertility disorder (Moderate, GenCC)
  • GWAS associations: 2
  • Clinical variants (ClinVar): 2 total — 1 likely-pathogenic
  • MANE Select transcript: NM_001282322

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:20438
Approved symbolRNF212B
Namering finger protein 212B
Location14q11.2
Locus typegene with protein product
StatusApproved
Ensembl geneENSG00000215277
Ensembl biotypeprotein_coding
OMIM621020
Entrez100507650

Gene structure

Transcript identifiers

Ensembl transcripts: 12 — 7 protein_coding, 4 protein_coding_CDS_not_defined, 1 nonsense_mediated_decay

ENST00000399905, ENST00000399910, ENST00000430154, ENST00000463881, ENST00000470456, ENST00000470818, ENST00000492355, ENST00000492621, ENST00000498441, ENST00000689421, ENST00000913744, ENST00000951077

RefSeq mRNA: 2 — MANE Select: NM_001282322 NM_001282322, NM_001370218

CCDS: CCDS61401

Canonical transcript exons

ENST00000430154 — 15 exons

ExonStartEnd
ENSE000015407382326266523262711
ENSE000015407392326065923260687
ENSE000015407402325988423259944
ENSE000015407442325854923258664
ENSE000015407462324432223244396
ENSE000015407482324325623243308
ENSE000024381682324034523240445
ENSE000034911072327060023270661
ENSE000035249942327282323273477
ENSE000035406232326892423268963
ENSE000036298072326292823262970
ENSE000036351092326986323269960
ENSE000036872682326417423264234
ENSE000037879412326462323264671
ENSE000039322682323793623238055

Expression profiles

Bgee: expression breadth ubiquitous, 157 present calls, max score 92.27.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.1144 / max 26.9472, expressed in 35 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter IDTPM avgSamples expressed
1388840.114435

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
kidney epitheliumUBERON:000481992.27gold quality
spermCL:000001991.52gold quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099189.05gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047382.58gold quality
right testisUBERON:000453478.03gold quality
left testisUBERON:000453377.65gold quality
testisUBERON:000047376.34gold quality
adult organismUBERON:000702372.61gold quality
adult mammalian kidneyUBERON:000008272.41gold quality
kidneyUBERON:000211371.26gold quality
pancreatic ductal cellCL:000207970.98silver quality
islet of LangerhansUBERON:000000668.21gold quality
cortex of kidneyUBERON:000122566.90gold quality
tibialis anteriorUBERON:000138566.54silver quality
metanephros cortexUBERON:001053363.34gold quality
calcaneal tendonUBERON:000370163.25gold quality
monocyteCL:000057663.09gold quality
leukocyteCL:000073862.89gold quality
stromal cell of endometriumCL:000225562.25gold quality
ileal mucosaUBERON:000033161.82silver quality
left lobe of thyroid glandUBERON:000112061.63gold quality
mucosa of stomachUBERON:000119961.49gold quality
sural nerveUBERON:001548861.09gold quality
right lobe of thyroid glandUBERON:000111960.76gold quality
thyroid glandUBERON:000204660.54gold quality
right coronary arteryUBERON:000162559.61gold quality
right uterine tubeUBERON:000130259.53gold quality
pancreasUBERON:000126458.41gold quality
metanephrosUBERON:000008158.40gold quality
tibial nerveUBERON:000132357.30gold quality

Single-cell (SCXA)

Detected in 3 experiment(s), a significant marker in 3.

ExperimentMarker?Max mean expression
E-GEOD-131882yes2066.65
E-CURD-119yes1985.40
E-ANND-3yes5.67

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

91 targeting RNF212B, 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-518D-5P100.0067.51979
HSA-MIR-518E-5P100.0067.66954
HSA-MIR-518F-5P100.0067.51979
HSA-MIR-519A-5P100.0067.66954
HSA-MIR-519B-5P100.0067.66954
HSA-MIR-519C-5P100.0067.66954
HSA-MIR-520C-5P100.0067.51979
HSA-MIR-522-5P100.0067.66954
HSA-MIR-523-5P100.0067.66954
HSA-MIR-526A-5P100.0067.51979
HSA-MIR-3646100.0073.565283
HSA-MIR-6851-5P100.0065.631294
HSA-MIR-6833-3P100.0070.633197
HSA-MIR-607799.9968.042299
HSA-MIR-450099.9972.722367
HSA-MIR-1213699.9872.815713
HSA-MIR-548N99.9871.944170
HSA-MIR-302C-5P99.9772.563642
HSA-MIR-6888-3P99.9765.951170
HSA-MIR-6755-5P99.9565.59464
HSA-MIR-651-3P99.9473.485177
HSA-MIR-9983-3P99.9471.483631
HSA-MIR-314399.9371.963104
HSA-MIR-568099.9169.833421
HSA-MIR-990299.8969.152250
HSA-MIR-129-5P99.8870.263273
HSA-MIR-449699.8868.892236
HSA-MIR-548AR-3P99.8571.263889
HSA-MIR-548AZ-5P99.8369.943230
HSA-MIR-548T-5P99.8369.913220

Literature-anchored findings (GeneRIF, showing 1)

  • A pathogenic variant in the uncharacterized RNF212B gene results in severe aneuploidy male infertility and repeated IVF failure. (PMID:37124137)

Cross-species orthologs

9 orthologs

OrganismSymbolGene ID
danio_reriornf212bENSDARG00000093723
mus_musculusRnf212bENSMUSG00000112858
rattus_norvegicusRnf212bENSRNOG00000066673
drosophila_melanogasternaryaFBGN0031018
drosophila_melanogasternenyaFBGN0051053
caenorhabditis_eleganszhp-3WBGENE00006976
caenorhabditis_eleganszhp-2WBGENE00008387
caenorhabditis_elegansWBGENE00012678
caenorhabditis_eleganszhp-1WBGENE00018867

Paralogs (1): RNF212 (ENSG00000178222)

Protein

Protein identifiers

E3 ubiquitin-protein ligase RNF212BA8MTL3 (reviewed: A8MTL3)

Alternative names: RING finger protein 212B

All UniProt accessions (5): A0A8I5QKV8, A8MTL3, A8MVE6, G3V2N7, H0YJB3

UniProt curated annotations — full annotation on UniProt →

Function. Ubiquitin E3 ligase that acts as a crucial factor for crossing-over (CO) formation during meiosis. Essential for normal prophase I progression and for ensuring appropriate CO designation in meiosis. Recruits key components of the cross-over machinery either directly ou indirectly, leading to the activation of the MutL-gamma complex. The function of RNF212B in CO designation is dependent on its catalytic activity.

Subunit / interactions. Homodimer.

Subcellular location. Chromosome.

Post-translational modifications. Autoubiquitinated.

Pathway. Protein modification; protein ubiquitination.

RefSeq proteins (2): NP_001269251, NP_001357147 (=MANE)

Domains & families (InterPro)

IDNameType
IPR017907Znf_RING_CSConserved_site
IPR042123Zip3/RNF212-likeFamily

UniProt features (11 total): compositionally biased region 4, sequence conflict 2, chain 1, zinc finger region 1, region of interest 1, coiled-coil region 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-A8MTL3-F167.100.34

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 69 (showing top): GOBP_MEIOTIC_CHROMOSOME_SEGREGATION, GOBP_CHROMOSOME_ORGANIZATION, GOBP_ORGANELLE_FISSION, GOBP_POST_TRANSLATIONAL_PROTEIN_MODIFICATION, GOBP_CHROMOSOME_ORGANIZATION_INVOLVED_IN_MEIOTIC_CELL_CYCLE, GOBP_HOMOLOGOUS_CHROMOSOME_SEGREGATION, GOBP_MEIOTIC_CELL_CYCLE_PROCESS, GOBP_HOMOLOGOUS_CHROMOSOME_PAIRING_AT_MEIOSIS, GOBP_NUCLEAR_CHROMOSOME_SEGREGATION, GOBP_MEIOTIC_CELL_CYCLE, GOBP_CELL_CYCLE_PROCESS, GOBP_DNA_METABOLIC_PROCESS, GOMF_ACYLTRANSFERASE_ACTIVITY, GOBP_DNA_RECOMBINATION, GOMF_SUMO_TRANSFERASE_ACTIVITY

GO Biological Process (5): homologous chromosome pairing at meiosis (GO:0007129), protein ubiquitination (GO:0016567), chiasma assembly (GO:0051026), reciprocal meiotic recombination (GO:0007131), meiotic cell cycle (GO:0051321)

GO Molecular Function (5): zinc ion binding (GO:0008270), SUMO transferase activity (GO:0019789), ubiquitin protein ligase activity (GO:0061630), transferase activity (GO:0016740), metal ion binding (GO:0046872)

GO Cellular Component (2): synaptonemal complex (GO:0000795), chromosome (GO:0005694)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
meiotic cell cycle process2
homologous chromosome segregation1
chromosome organization involved in meiotic cell cycle1
protein modification by small protein conjugation1
homologous chromosome pairing at meiosis1
reciprocal meiotic recombination1
cellular component assembly1
meiosis I1
reciprocal homologous recombination1
cell cycle1
sexual reproduction1
reproductive process1
meiotic nuclear division1
transition metal ion binding1
ubiquitin-like protein transferase activity1
ubiquitin-protein transferase activity1
ubiquitin-like protein ligase activity1
catalytic activity1
cation binding1
synaptonemal structure1
intracellular membraneless organelle1

Protein interactions and networks

STRING

192 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
RNF212BHFM1A2PYH4626
RNF212BOR10G3Q8NGC4615
RNF212BOR10G2Q8NGC3613
RNF212BMSH4O15457605
RNF212BREC114Q7Z4M0591
RNF212BREC8O95072573
RNF212BTEX11Q8IYF3557
RNF212BSPO11Q9Y5K1520
RNF212BMLH3P49751470
RNF212BTOX4O94842456
RNF212BPRDM9Q9NQV7447
RNF212BSUPT16HQ9Y5B9446
RNF212BCPLX1O14810446
RNF212BCCNB1IP1Q9NPC3419
RNF212BSHOC1Q5VXU9411

IntAct

0 interactions, top by confidence:

ESM2 similar proteins: A0A1W2P884, A0M8S4, A0M8T5, A5PLL1, A8MTL3, B9EJA2, D3Z423, F1QZ88, F6TQD1, O54916, O60296, P0C6C1, Q00PJ1, Q07DV1, Q07DX4, Q07E15, Q07E28, Q07E41, Q09YG9, Q09YI1, Q09YK4, Q108T9, Q13625, Q2IBB2, Q2IBD4, Q2IBE6, Q2IBF7, Q2QLA2, Q2QLB3, Q2QLF8, Q2VUH7, Q3UIL6, Q3UUF8, Q53HC0, Q5PQ89, Q5RBV9, Q5RJ80, Q5SZL2, Q6IQ23, Q6P2H3

Diamond homologs: A8MTL3, C6KRL6, D3Z423, Q495C1, Q5RBV9, F6TQD1, Q8MYP1

SIGNOR signaling

1 interactions.

AEffectBMechanism
Ub:E2“up-regulates activity”RNF212Bubiquitination

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic1
Uncertain significance0
Likely benign1
Benign0

Top pathogenic / likely-pathogenic (1)

Variant IDHGVSClassification
3062225NM_001282322.3(RNF212B):c.448C>T (p.Arg150Ter)Likely pathogenic

SpliceAI

2406 predictions. Top by Δscore:

VariantEffectΔscore
14:23230160:G:GTdonor_gain1.0000
14:23243254:A:AGacceptor_gain1.0000
14:23243255:G:GGacceptor_gain1.0000
14:23243255:GAA:Gacceptor_gain1.0000
14:23243255:GAAAA:Gacceptor_gain1.0000
14:23243309:G:GGdonor_gain1.0000
14:23244320:A:AGacceptor_gain1.0000
14:23244321:G:GGacceptor_gain1.0000
14:23244321:GCT:Gacceptor_gain1.0000
14:23185491:G:GGdonor_gain0.9900
14:23240343:A:AGacceptor_gain0.9900
14:23240344:G:GGacceptor_gain0.9900
14:23243250:TCCCA:Tacceptor_loss0.9900
14:23243251:CCCA:Cacceptor_loss0.9900
14:23243252:CCA:Cacceptor_loss0.9900
14:23243254:AGAA:Aacceptor_loss0.9900
14:23243255:G:Tacceptor_loss0.9900
14:23243255:GA:Gacceptor_gain0.9900
14:23243255:GAAA:Gacceptor_gain0.9900
14:23244318:GTA:Gacceptor_loss0.9900
14:23244319:TA:Tacceptor_loss0.9900
14:23244321:GCTGA:Gacceptor_gain0.9900
14:23244392:CTCAG:Cdonor_loss0.9900
14:23244393:TCAGG:Tdonor_loss0.9900
14:23244394:CAG:Cdonor_loss0.9900
14:23244395:AGGTA:Adonor_loss0.9900
14:23244396:G:GCdonor_loss0.9900
14:23244397:G:GAdonor_loss0.9900
14:23244398:T:Adonor_loss0.9900
14:23264164:C:Gacceptor_gain0.9900

AlphaMissense

1948 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
14:23258558:T:CF80L0.997
14:23258560:C:AF80L0.997
14:23258560:C:GF80L0.997
14:23240361:T:CC6R0.995
14:23258559:T:CF80S0.995
14:23240401:T:AV19D0.994
14:23240424:T:CC27R0.994
14:23240361:T:AC6S0.993
14:23240362:G:AC6Y0.993
14:23240362:G:CC6S0.993
14:23240363:C:GC6W0.993
14:23240352:T:AW3R0.992
14:23240352:T:CW3R0.992
14:23240370:T:AC9S0.992
14:23240371:G:CC9S0.992
14:23240409:T:CC22R0.992
14:23243261:T:CC36R0.992
14:23258583:T:CL88P0.992
14:23240362:G:TC6F0.991
14:23240370:T:CC9R0.991
14:23258562:A:CQ81P0.991
14:23240410:G:AC22Y0.990
14:23244347:T:CF60S0.990
14:23240409:T:AC22S0.988
14:23240410:G:CC22S0.988
14:23240425:G:AC27Y0.988
14:23240433:T:CC30R0.988
14:23243270:T:CC39R0.988
14:23258580:T:CL87P0.988
14:23240358:C:GH5D0.987

dbSNP variants (sampled 300 via entrez): RS1000048658 (14:23231795 A>G), RS1000055152 (14:23194197 G>T), RS1000155947 (14:23190976 G>C), RS1000165876 (14:23190734 G>A,C), RS1000168744 (14:23273942 A>G), RS1000177844 (14:23268277 C>T), RS1000244086 (14:23234920 A>G,T), RS1000247811 (14:23220599 G>A), RS1000317047 (14:23266706 C>T), RS1000327002 (14:23192660 A>G,T), RS1000349060 (14:23186317 T>A), RS1000349551 (14:23196491 G>A), RS1000367548 (14:23226330 T>A,G), RS1000384240 (14:23244246 T>A), RS1000404372 (14:23261617 C>G,T)

Disease associations

OMIM: gene MIM:621020 | disease phenotypes:

GenCC curated gene-disease

DiseaseClassificationInheritance
infertility disorderModerateAutosomal recessive

Mondo (2): female infertility (MONDO:0021124), infertility disorder (MONDO:0005047)

Orphanet (0):

HPO phenotypes

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

GWAS associations

2 associations (top):

StudyTraitp-value
GCST010244_81Triglyceride levels2.000000e-09
GCST90002402_226Platelet count8.000000e-09

EFO canonical traits (2, from GWAS)

EFO IDTrait name
EFO:0004530triglyceride measurement
EFO:0004309platelet count

MeSH disease descriptors (2)

DescriptorNameTree numbers
D007246InfertilityC12.100.750
D007247Infertility, FemaleC12.050.351.500.498; C12.100.250.498; C12.100.750.350

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

PharmGKB variants

1 variants.

VariantGenesLevelScore#Clin annotsDrugs
rs7141505RNF212B, SLC7A80.000

CTD chemical–gene interactions

7 total (human), top 7 by PubMed support.

ChemicalActions (top 5)PubMed papers
benzo(e)pyrenedecreases methylation1
ferrous chloridedecreases expression1
aflatoxin B2decreases methylation1
S-(1,2-dichlorovinyl)cysteineaffects response to substance, increases expression, affects cotreatment1
Benzo(a)pyreneaffects methylation1
Lipopolysaccharidesaffects response to substance, increases expression, affects cotreatment1
Methapyrilenedecreases methylation1

Clinical trials (associated diseases)

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

TrialPhaseStatusTitle
NCT01388907PHASE4COMPLETEDEfficacity Assessment of PREVADH® in Adhesion Prevention in Gynaecologic Surgery
NCT01430650PHASE4COMPLETEDEndometrial Priming for Embryo Transfer
NCT02607319PHASE4COMPLETEDLow Molecular Weight Heparin to Improve Pregnancy Outcome in Patients With Recurrent Implantation Failure
NCT03169166PHASE4COMPLETEDThe Use of GnRH Agonist Trigger for Final Follicle Maturation in Women Undergoing Assisted Reproductive Technologies
NCT03177122PHASE4UNKNOWNMyo-Inositol- Based Co-treatment in Women With PCOS Undergoing Assisted Reproductive Technology
NCT03477929PHASE4UNKNOWNCetrorelix and Ganirelix Flexible Protocol for (IVF)
NCT03619707PHASE4COMPLETEDOral Versus Vaginal Progesterone in the Luteal Support in Cryo-warmed Embryo Transfer Cycles
NCT03846544PHASE4COMPLETEDDouble Pick up in Poor Prognosis Women
NCT05725512PHASE4RECRUITINGPrednisolone Administration in Patients With Unexplained REcurrent MIscarriages
NCT06195163PHASE4NOT_YET_RECRUITINGTRAP Study: Testosterone for Androgen Receptor Polymorphism
NCT06763926PHASE4NOT_YET_RECRUITINGIntranasal Nafarelin For Triggering Oocyte Maturation
NCT01577472PHASE4COMPLETEDEfficacy Study Comparing the Effect of Clomiphencitrate to an Antagonist Protocol
NCT01791751PHASE4COMPLETEDImpact of Clomiphene Citrate Administration During the Early Luteal Phase on Endocrine Profile in IVF Cycles
NCT02070198PHASE4UNKNOWNLong Acting FSH Plus Antagonist Versus Daily FSH Plus Antagonist Versus Short Agonist Protocol in Poor Responders Undergoing IVF
NCT02328924PHASE4COMPLETEDThere is a Value of Luteinizing Hormone Predictive of in Vitro Fertilization Treatment Outcome in Antagonist Protocols?
NCT03057574PHASE4UNKNOWNGonapure® in Multifollicular Stimulation in Egyptian Women Undergoing IVF/ICSI
NCT05197374PHASE4COMPLETEDEffect of Estradiol Pretreatment on Antagonist ICSI Cycles
NCT05281341PHASE4COMPLETEDEffect of GH Administration in Poor Responders Undergoing Intracytoplasmic Sperm Injection (ICSI)
NCT05286554PHASE4COMPLETEDAddition of Gonadotropin Releasing Hormone Agonist to Luteal Phase Support
NCT05608590PHASE4UNKNOWNWhat is the Best Moment for Performing an HSG in Women With a Unfulfilled Childwish
NCT05753098PHASE4COMPLETEDEffect of Sildenafil Citrate Compared to Estrogen as Adjuvant Therapy for Unexplained Infertility
NCT06434233PHASE4RECRUITINGOpioid Use After Laparoscopic Salpingectomy
NCT06684951PHASE4COMPLETEDEffects of Intrauterine Flushing With Human Chorionic Gonadotropin on ICSI Outcome
NCT06921395PHASE4RECRUITINGPhase IV Study to Evaluate the Efficacy and Safety of Fang Le Shu Compared to Guo Na Fen for Controlled Ovarian Stimulation in Infertile Women Undergoing in Vitro Fertilization-embryo Transfer (IVF-ET).
NCT00749853PHASE3SUSPENDEDEfficacy of Ovarian Stimulation Based on FSHR Genotype Status
NCT03238092PHASE3UNKNOWNComparison Between Testosterone and Estradiol Over the Homogenization of Follicular Cohort
NCT03803228PHASE3COMPLETEDDual Ovarian Stimulation (DUOSTIM) for Poor Ovarian Responders
NCT01850030PHASE3COMPLETEDA Multicenter Study Comparing the Efficacy, Safety and Tolerability of Oral Dydrogesterone 30 mg Daily Versus Intravaginal Micronized Progesterone Capsules 600 mg Daily for Luteal Support in In-Vitro Fertilization
NCT02175498PHASE3COMPLETEDEffectiveness of Homeopathic Treatment in Female Infertility
NCT02491437PHASE3COMPLETEDA Study Comparing the Efficacy, Safety and Tolerability of Oral Dydrogesterone 30 mg Daily Versus Crinone 8% Intravaginal Progesterone Gel 90 mg Daily for Luteal Support in In-Vitro Fertilization (LOTUS II)
NCT03429621PHASE3COMPLETEDEffect of Simethicone on Reducing Bowel Interference During Tubal Resection
NCT03542331PHASE3UNKNOWNEndometrial Effects of Lipiodol
NCT03767569PHASE3UNKNOWNMyo-inositol as Pretreatment in Hyperandrogenic PCOS Patients
NCT03862586PHASE3COMPLETEDNAC Effect on Hox Genes Expressions in RIF
NCT05266924PHASE3UNKNOWNRecombinant Follicle-stimulating Hormone in Treatment for Infertility
NCT05460858PHASE3UNKNOWNNAC Effect on Infertile Women With Endometrioma
NCT04701034PHASE2COMPLETEDIntravenous Immunoglobulin and Prednisolone for RPL After ART.
NCT04850261PHASE2WITHDRAWNInjection Free IVF
NCT06997900PHASE2RECRUITINGMenopur And Rekovelle Combination Study Version 2.0
NCT01354886PHASE1COMPLETEDSingle Dose FSH-GEX™ in Healthy Volunteers