FANCD2OS

gene
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Also known as MGC40179

Summary

FANCD2OS (FANCD2 opposite strand, HGNC:28623) is a protein-coding gene on chromosome 3p25.3, encoding FANCD2 opposite strand protein (Q96PS1). Reduces testosterone levels by inhibiting steroidogenic enzymes and by promoting apoptosis in Leydig cells.

This gene encodes a conserved protein of unknown function.

Source: NCBI Gene 115795 — RefSeq curated summary.

At a glance

  • GWAS associations: 2
  • Clinical variants (ClinVar): 97 total — 4 pathogenic, 2 likely-pathogenic
  • MANE Select transcript: NM_001164839

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:28623
Approved symbolFANCD2OS
NameFANCD2 opposite strand
Location3p25.3
Locus typegene with protein product
StatusApproved
AliasesMGC40179
Ensembl geneENSG00000163705
Ensembl biotypeprotein_coding
OMIM621082
Entrez115795

Gene structure

Transcript identifiers

Ensembl transcripts: 6 — 3 protein_coding_CDS_not_defined, 3 protein_coding

ENST00000431315, ENST00000436517, ENST00000450616, ENST00000450660, ENST00000453223, ENST00000524279

RefSeq mRNA: 2 — MANE Select: NM_001164839 NM_001164839, NM_173472

CCDS: CCDS2596

Canonical transcript exons

ENST00000450660 — 2 exons

ExonStartEnd
ENSE000016446551010801510108255
ENSE000020925061010393710104782

Expression profiles

Bgee: expression breadth ubiquitous, 120 present calls, max score 95.73.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.1185 / max 115.9288, expressed in 4 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter IDTPM avgSamples expressed
410190.10864
410200.00983

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
left testisUBERON:000453395.73gold quality
right testisUBERON:000453495.41gold quality
testisUBERON:000047392.08gold quality
pancreatic ductal cellCL:000207992.06silver quality
spermCL:000001986.58gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047383.61gold quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099180.94gold quality
adult organismUBERON:000702379.72gold quality
ileal mucosaUBERON:000033174.75silver quality
myocardiumUBERON:000234970.48gold quality
cardiac muscle of right atriumUBERON:000337969.83gold quality
left ventricle myocardiumUBERON:000656669.58gold quality
deltoidUBERON:000147666.65gold quality
upper arm skinUBERON:000426365.32gold quality
skeletal muscle tissue of rectus abdominisUBERON:000451164.20gold quality
quadriceps femorisUBERON:000137763.99gold quality
upper leg skinUBERON:000426262.17silver quality
vastus lateralisUBERON:000137961.97gold quality
skeletal muscle tissue of biceps brachiiUBERON:000450261.54gold quality
tendon of biceps brachiiUBERON:000818860.93gold quality
heart right ventricleUBERON:000208060.70gold quality
nasal cavity epitheliumUBERON:000538460.07gold quality
biceps brachiiUBERON:000150759.63gold quality
superficial temporal arteryUBERON:000161458.76gold quality
gingival epitheliumUBERON:000194955.72gold quality
lateral globus pallidusUBERON:000247654.73gold quality
skeletal muscle tissueUBERON:000113454.68gold quality
gingivaUBERON:000182854.50gold quality
parotid glandUBERON:000183154.45gold quality
muscle tissueUBERON:000238554.40silver quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3yes4.21

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

34 targeting FANCD2OS, 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-3134100.0066.43777
HSA-MIR-453499.9966.581907
HSA-MIR-808299.9567.271170
HSA-MIR-9983-3P99.9471.483631
HSA-MIR-153-5P99.8973.866317
HSA-MIR-129-5P99.8870.263273
HSA-MIR-6857-5P99.8765.32985
HSA-MIR-10395-5P99.8667.35676
HSA-MIR-6885-3P99.7570.363187
HSA-MIR-430699.7270.503630
HSA-MIR-425599.7267.701541
HSA-MIR-580-3P99.6769.231841
HSA-MIR-3158-5P99.6567.511763
HSA-MIR-122B-5P99.4670.811457
HSA-MIR-425199.4069.193363
HSA-MIR-185-5P99.3568.602497
HSA-MIR-464499.3569.122514
HSA-MIR-5582-5P99.2771.421879
HSA-MIR-1911-5P98.9267.53325
HSA-MIR-445098.2668.35725
HSA-MIR-365097.8864.89693
HSA-MIR-4433A-3P97.7562.821435
HSA-MIR-299-3P97.7366.67773
HSA-MIR-425397.4865.11692
HSA-MIR-6862-5P97.4864.84713
HSA-MIR-519296.8963.35879
HSA-MIR-4703-3P96.6868.61545
HSA-MIR-449196.5366.20935
HSA-MIR-465796.5366.57895
HSA-MIR-4761-3P96.2766.26524

Cross-species orthologs

6 orthologs

OrganismSymbolGene ID
mus_musculusFancd2osENSMUSG00000033963
rattus_norvegicusFancd2osENSRNOG00000010177
rattus_norvegicusENSRNOG00000072822
rattus_norvegicusFancd2osl1ENSRNOG00000077755
rattus_norvegicusENSRNOG00000085190
rattus_norvegicusENSRNOG00000088812

Protein

Protein identifiers

FANCD2 opposite strand proteinQ96PS1 (reviewed: Q96PS1)

Alternative names: Fanconi anemia group D2 protein opposite strand transcript protein

All UniProt accessions (2): Q96PS1, H0YBI7

UniProt curated annotations — full annotation on UniProt →

Function. Reduces testosterone levels by inhibiting steroidogenic enzymes and by promoting apoptosis in Leydig cells.

Subcellular location. Cytoplasm.

RefSeq proteins (2): NP_001158311, NP_775743 (=MANE)

Domains & families (InterPro)

IDNameType
IPR027966FANCD2OSFamily

Pfam: PF15124

UniProt features (1 total): chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q96PS1-F161.310.15

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 59 (showing top): GOBP_NEGATIVE_REGULATION_OF_LIPID_METABOLIC_PROCESS, CMYB_01, GOBP_NEGATIVE_REGULATION_OF_STEROID_METABOLIC_PROCESS, GOBP_NEGATIVE_REGULATION_OF_LIPID_BIOSYNTHETIC_PROCESS, GOBP_KETONE_METABOLIC_PROCESS, GOBP_REGULATION_OF_LIPID_BIOSYNTHETIC_PROCESS, GOBP_SMALL_MOLECULE_BIOSYNTHETIC_PROCESS, GOBP_REGULATION_OF_LIPID_METABOLIC_PROCESS, GOBP_REGULATION_OF_KETONE_METABOLIC_PROCESS, GOBP_STEROID_BIOSYNTHETIC_PROCESS, GOBP_LIPID_METABOLIC_PROCESS, GOBP_KETONE_BIOSYNTHETIC_PROCESS, GOBP_LIPID_BIOSYNTHETIC_PROCESS, GOBP_REGULATION_OF_STEROID_BIOSYNTHETIC_PROCESS, GOBP_REGULATION_OF_STEROID_METABOLIC_PROCESS

GO Biological Process (1): negative regulation of testosterone biosynthetic process (GO:2000225)

GO Molecular Function (0):

GO Cellular Component (1): cytoplasm (GO:0005737)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
negative regulation of steroid biosynthetic process1
testosterone biosynthetic process1
negative regulation of small molecule metabolic process1
regulation of testosterone biosynthetic process1
intracellular anatomical structure1
cellular anatomical structure1

Protein interactions and networks

STRING

320 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
FANCD2OSTRIML1Q8N9V2514
FANCD2OSPRRT3Q5FWE3479
FANCD2OSTATDN2Q93075446
FANCD2OSCCDC152Q4G0S7443
FANCD2OSCPNE9Q8IYJ1433
FANCD2OSTHUMPD3Q9BV44419
FANCD2OSSSUH2Q9Y2M2419
FANCD2OSSP2Q02086414
FANCD2OSTMEM232C9JQI7390
FANCD2OSLHFPL4Q7Z7J7380
FANCD2OSRPUSD3Q6P087370
FANCD2OSJAGN1Q8N5M9359
FANCD2OSTTLL3Q9Y4R7354
FANCD2OSNARS1O43776345
FANCD2OSERCC6L2Q5T890336

IntAct

4 interactions, top by confidence:

ABTypeScore
FANCD2OSCNOT1psi-mi:“MI:0914”(association)0.530

BioGRID (25): MINK1 (Affinity Capture-MS), RQCD1 (Affinity Capture-MS), CNOT3 (Affinity Capture-MS), MAP4K4 (Affinity Capture-MS), TROAP (Affinity Capture-MS), CNOT10 (Affinity Capture-MS), FBRS (Affinity Capture-MS), BTG3 (Affinity Capture-MS), RNF219 (Affinity Capture-MS), KIAA0232 (Affinity Capture-MS), CNOT6 (Affinity Capture-MS), CNOT7 (Affinity Capture-MS), DYRK1A (Affinity Capture-MS), CNOT11 (Affinity Capture-MS), TNKS1BP1 (Affinity Capture-MS)

ESM2 similar proteins: A0A1B0GTK4, A0JNL8, A2RU37, A4D1N5, B1A0U8, B1ANY3, F2Z398, G3V211, J3KSC0, J3QMY9, O14603, O93195, O95411, P03414, P0C7M3, P37200, P47939, P47940, P49671, P92561, Q02919, Q32KZ5, Q4G0G2, Q5SR53, Q5T0J3, Q5T6R2, Q66669, Q66HF0, Q6AWC8, Q6DGF6, Q6ZP68, Q6ZSR6, Q7L4S7, Q86UQ5, Q86Y29, Q8BGX4, Q8N326, Q8N4M7, Q8N6C7, Q8N769

Diamond homologs: Q32KZ5, Q96PS1, Q9D4K4

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic4
Likely pathogenic2
Uncertain significance52
Likely benign24
Benign10

Top pathogenic / likely-pathogenic (6)

Variant IDHGVSClassification
1685811NM_001018115.3(FANCD2):c.3777+1G>TPathogenic
2807269NM_001018115.3(FANCD2):c.3693del (p.Phe1231fs)Pathogenic
456559NC_000003.12:g.(?10064723)(10149971_?)delPathogenic
929670NM_001018115.3(FANCD2):c.3803G>A (p.Trp1268Ter)Pathogenic
1345612NC_000003.11:g.(?10132039)(10132856_?)delLikely pathogenic
2744051NM_001018115.3(FANCD2):c.3224+1G>CLikely pathogenic

SpliceAI

2283 predictions. Top by Δscore:

VariantEffectΔscore
3:10081344:A:AGacceptor_gain1.0000
3:10081345:G:GTacceptor_gain1.0000
3:10081345:GT:Gacceptor_gain1.0000
3:10081460:GCTTG:Gdonor_gain1.0000
3:10081461:CTTGG:Cdonor_loss1.0000
3:10081462:TTGG:Tdonor_loss1.0000
3:10081463:TGGT:Tdonor_loss1.0000
3:10081465:G:Cdonor_loss1.0000
3:10081465:G:GGdonor_gain1.0000
3:10081466:T:TCdonor_loss1.0000
3:10081467:AA:Adonor_loss1.0000
3:10085811:GGA:Gacceptor_gain1.0000
3:10088821:A:AGacceptor_gain1.0000
3:10088825:CAG:Cacceptor_loss1.0000
3:10088826:A:AGacceptor_gain1.0000
3:10088826:A:Gacceptor_loss1.0000
3:10088827:G:GTacceptor_gain1.0000
3:10088827:GT:Gacceptor_gain1.0000
3:10088827:GTA:Gacceptor_gain1.0000
3:10088827:GTAT:Gacceptor_gain1.0000
3:10088827:GTATC:Gacceptor_gain1.0000
3:10088949:AGGTA:Adonor_loss1.0000
3:10088951:G:Cdonor_loss1.0000
3:10088952:T:Gdonor_loss1.0000
3:10090314:C:CAacceptor_gain1.0000
3:10090316:T:TAacceptor_gain1.0000
3:10090318:T:TAacceptor_gain1.0000
3:10081344:AGT:Aacceptor_gain0.9900
3:10081345:GTG:Gacceptor_gain0.9900
3:10081345:GTGT:Gacceptor_gain0.9900

AlphaMissense

1149 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
3:10104397:A:CF126L0.984
3:10104397:A:TF126L0.984
3:10104399:A:GF126L0.984
3:10104470:A:TV102D0.975
3:10104270:A:GC169R0.972
3:10104321:A:GC152R0.969
3:10104308:A:GL156P0.966
3:10104398:A:GF126S0.966
3:10104466:A:CF103L0.966
3:10104466:A:TF103L0.966
3:10104468:A:GF103L0.966
3:10104720:A:GW19R0.966
3:10104720:A:TW19R0.966
3:10104305:C:GR157P0.965
3:10104262:A:CF171L0.962
3:10104262:A:TF171L0.962
3:10104264:A:GF171L0.962
3:10104274:T:AK167N0.960
3:10104274:T:GK167N0.960
3:10104285:C:GA164P0.954
3:10104756:A:GW7R0.954
3:10104756:A:TW7R0.954
3:10104296:A:GL160P0.952
3:10104275:T:AK167I0.951
3:10104488:A:TL96H0.951
3:10104290:A:GL162P0.949
3:10104279:A:CY166D0.948
3:10104288:A:CY163D0.945
3:10104488:A:GL96P0.941
3:10104401:G:TA125D0.939

dbSNP variants (sampled 300 via entrez): RS1000088984 (3:10095431 A>C), RS1000094692 (3:10103647 T>C), RS1000142282 (3:10108712 G>A), RS1000158209 (3:10106464 G>A), RS1000254003 (3:10085865 T>A), RS1000278037 (3:10106799 G>A,T), RS1000437618 (3:10094211 T>C), RS1000474147 (3:10107452 A>AT), RS1000704082 (3:10101524 G>A,T), RS1000881167 (3:10082400 C>T), RS1000992041 (3:10082147 A>G), RS1001077491 (3:10081282 C>A,T), RS1001129479 (3:10100783 A>G), RS1001285026 (3:10094769 G>A), RS1001355687 (3:10107444 C>G)

Disease associations

OMIM: gene MIM:621082 | disease phenotypes: MIM:227650, MIM:227646, MIM:193300, MIM:263400

GenCC curated gene-disease

Mondo (5): Fanconi anemia (MONDO:0019391), Fanconi anemia complementation group D2 (MONDO:0009214), hereditary breast ovarian cancer syndrome (MONDO:0003582), von Hippel-Lindau disease (MONDO:0008667), Chuvash polycythemia (MONDO:0009892)

Orphanet (4): Fanconi anemia (Orphanet:84), Hereditary breast and/or ovarian cancer syndrome (Orphanet:145), Chuvash erythrocytosis (Orphanet:238557), Von Hippel-Lindau disease (Orphanet:892)

HPO phenotypes

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

GWAS associations

2 associations (top):

StudyTraitp-value
GCST002422_5Alzheimer’s disease2.000000e-06
GCST003264_1052Post bronchodilator FEV1/FVC ratio3.000000e-06

EFO canonical traits (1, from GWAS)

EFO IDTrait name
EFO:0004713FEV/FVC ratio

MeSH disease descriptors (4)

DescriptorNameTree numbers
D005199Fanconi AnemiaC15.378.050.085.080.280; C15.378.190.223.500.500.280; C16.320.077.280; C18.452.284.280
D061325Hereditary Breast and Ovarian Cancer SyndromeC04.588.180.483; C04.588.322.455.431; C04.700.517; C12.050.351.500.056.630.705.431; C12.050.351.937.418.685.431; C12.100.250.056.630.705.431; C12.900.418.685.431; C16.320.700.517; C17.800.090.500.483; C19.344.410.431; C19.391.630.705.431
D006623von Hippel-Lindau DiseaseC10.562.925; C14.907.077.925; C16.131.077.245.750; C16.320.184.750
C563918Erythrocytosis, Familial, 2 (supp.)

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

5 total (human), top 5 by PubMed support.

ChemicalActions (top 5)PubMed papers
sodium arsenitedecreases expression, increases expression2
Arbutindecreases expression1
Arsenicaffects methylation1
Benzo(a)pyreneaffects methylation1
Valproic Acidincreases methylation1

Clinical trials (associated diseases)

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

TrialPhaseStatusTitle
NCT02562170PHASE4COMPLETEDProtexa® Versus TiLoopBra® in Immediate Breast Reconstruction- A Pilot Study
NCT06519786PHASE3UNKNOWNSafety and Efficacy of Metformin for Treatment of Cytopenia in Children and Adolescents With Fanconi Anemia
NCT00673335PHASE3COMPLETEDLetrozole in Preventing Breast Cancer in Postmenopausal Women With a BRCA1 or BRCA2 Mutation
NCT00685256PHASE3COMPLETEDStandard Genetic Counseling With or Without a Decision Guide in Improving Communication Between Mothers Undergoing BRCA1/2 Testing and Their Minor-Age Children
NCT03162276PHASE3UNKNOWNTrial of Inquiry Based Stress Reduction (IBSR) Program for BRCA1/2 Mutation Carriers
NCT00000603PHASE2COMPLETEDCord Blood Stem Cell Transplantation Study (COBLT)
NCT00001749PHASE2COMPLETEDMedical Treatment for Diamond Blackfan Anemia
NCT00004787PHASE2COMPLETEDPhase II Pilot Study of Granulocyte Colony-Stimulating Factor for Inherited Bone Marrow Failure Syndromes
NCT00053989PHASE2COMPLETEDNMA Allogeneic Hematopoietic Cell Transplant in Hematologic Cancer/Disorders
NCT00084695PHASE2UNKNOWNUmbilical Cord Blood for Stem Cell Transplantation in Treating Young Patients With Malignant or Nonmalignant Diseases
NCT00258427PHASE2COMPLETEDHematopoietic Stem Cell Transplantation in High Risk Patients With Fanconi Anemia
NCT00453388PHASE2COMPLETEDFludarabine Phosphate, Cyclophosphamide, and Total-Body Irradiation Followed by Donor Bone Marrow Transplant, Mycophenolate Mofetil, and Cyclosporine in Treating Patients With Fanconi Anemia
NCT01071239PHASE2COMPLETEDHematopoietic Stem Cell Transplant for Fanconi Anemia
NCT02143830PHASE2RECRUITINGHSCT for Patients With Fanconi Anemia Using Risk-Adjusted Chemotherapy
NCT02931071PHASE2COMPLETEDClinical Phase II Trial to Evaluate CD34+ Cells Mobilization and Collection in Patients With Fanconi Anemia for Subsequent Transduction With a Lentiviral Vector Carring FANCA Gene. FANCOSTEM-1
NCT03206086PHASE2ACTIVE_NOT_RECRUITINGEltrombopag for People With Fanconi Anemia
NCT03398824PHASE2COMPLETEDPilot Study of Metformin for Patients With Fanconi Anemia
NCT03476330PHASE2COMPLETEDQuercetin Chemoprevention for Squamous Cell Carcinoma in Patients With Fanconi Anemia
NCT03579875PHASE2RECRUITINGAlpha/Beta TCD HCT in Patients With Inherited BMF Disorders
NCT03600909PHASE2TERMINATEDA Study of the Effect of Blood Stem Cell Transplant After Chemotherapy Alone in Patients With Fanconi Anemia
NCT04232085PHASE2RECRUITINGRegenerative Medicine to Restore Hematopoiesis and Immune Function in Immunodeficiencies and Inherited Bone Marrow Failures
NCT06045052PHASE2COMPLETEDEltrombopag for Treatment of Fanconi Anemia
NCT00253539PHASE2COMPLETEDArzoxifene or Tamoxifen in Preventing Breast Cancer in Premenopausal Women at High Risk for Breast Cancer
NCT00305695PHASE2COMPLETEDZoledronate or Observation in Maintaining Bone Mineral Density in Patients Who Are Undergoing Surgery to Remove Both Ovaries
NCT00321633PHASE2COMPLETEDCarboplatin or Docetaxel in Treating Women With Metastatic Genetic Breast Cancer
NCT01333748PHASE2COMPLETEDSearch Allelic Imbalance of Expression of BRCA Genes in Hereditary Risk of Breast and/or Ovarian Cancer
NCT01367639PHASE2COMPLETEDTrial of Inquiry Based Stress Reduction (IBSR) Program for BRCA1/2 Mutation Carriers
NCT00001399PHASE1COMPLETEDGene Therapy for the Treatment of Fanconi’s Anemia Type C
NCT00005896PHASE1UNKNOWNPhase I Pilot Study of CD34 Enriched, Fanconi’s Anemia Complementation Group C Gene Transduced Autologous Peripheral Blood Stem Cell Transplantation in Patients With Fanconi’s Anemia
NCT00006127PHASE1UNKNOWNPhase I Study of Amifostine in Patients With Bone Marrow Failure Related to Fanconi’s Anemia
NCT00093743PHASE1COMPLETEDLow-Dose Total-Body Irradiation and Fludarabine Phosphate Followed by Unrelated Donor Stem Cell Transplant in Treating Patients With Fanconi Anemia
NCT00243399PHASE1COMPLETEDOxandrolone for the Treatment of Bone Marrow Aplasia in Fanconi Anemia
NCT00272857PHASE1COMPLETEDBone Marrow Cell Gene Transfer in Individuals With Fanconi Anemia
NCT00317876PHASE1COMPLETEDCyclophosphamide in Treating Patients Who Are Undergoing a Donor Bone Marrow Transplant for Fanconi’s Anemia
NCT00586274PHASE1TERMINATEDUse of Rft5-Dga to Deplete Alloreactive Cells for Pts With Fanconi Anemia After Haploidentical SCT
NCT01331018PHASE1TERMINATEDGene Therapy for Fanconi Anemia
NCT01720147PHASE1COMPLETEDQuercetin in Children With Fanconi Anemia; a Pilot Study
NCT01917708PHASE1COMPLETEDBone Marrow Transplant With Abatacept for Non-Malignant Diseases
NCT00535119PHASE1COMPLETEDVeliparib, Carboplatin, and Paclitaxel in Treating Patients With Advanced Solid Cancer
NCT00892736PHASE1COMPLETEDVeliparib in Treating Patients With Malignant Solid Tumors That Do Not Respond to Previous Therapy