YRDC

gene
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Also known as FLJ23476IRIPSUA5

Summary

YRDC (yrdC N6-threonylcarbamoyltransferase domain containing, HGNC:28905) is a protein-coding gene on chromosome 1p34.3, encoding Threonylcarbamoyl-AMP synthase (Q86U90). Cytoplasmic and mitochondrial threonylcarbamoyl-AMP synthase required for the formation of a threonylcarbamoyl group on adenosine at position 37 (t(6)A37) in tRNAs that read codons beginning with adenine. It is a selective cancer dependency (DepMap: 86.8% of cell lines).

Enables L-threonylcarbamoyladenylate synthase. Involved in tRNA threonylcarbamoyladenosine modification. Acts upstream of or within negative regulation of transport. Is active in mitochondrion. Implicated in Galloway-Mowat syndrome.

Source: NCBI Gene 79693 — RefSeq curated summary.

At a glance

  • Gene–disease (curated): Galloway-Mowat syndrome 10 (Strong, GenCC)
  • GWAS associations: 1
  • Clinical variants (ClinVar): 59 total — 3 pathogenic
  • Phenotypes (HPO): 43
  • Cancer dependency (DepMap): dependent in 86.8% of screened cell lines
  • MANE Select transcript: NM_024640

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:28905
Approved symbolYRDC
NameyrdC N6-threonylcarbamoyltransferase domain containing
Location1p34.3
Locus typegene with protein product
StatusApproved
AliasesFLJ23476, IRIP, SUA5
Ensembl geneENSG00000196449
Ensembl biotypeprotein_coding
OMIM612276
Entrez79693

Gene structure

Transcript identifiers

Ensembl transcripts: 2 — 2 protein_coding

ENST00000373044, ENST00000882854

RefSeq mRNA: 1 — MANE Select: NM_024640 NM_024640

CCDS: CCDS30675

Canonical transcript exons

ENST00000373044 — 5 exons

ExonStartEnd
ENSE000014030243780710137807215
ENSE000014237653780685737806976
ENSE000014262853780430237804444
ENSE000014593963780294537803997
ENSE000014593973780779237808208

Expression profiles

Bgee: expression breadth ubiquitous, 255 present calls, max score 93.26.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 18.2990 / max 446.2443, expressed in 1812 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter IDTPM avgSamples expressed
1180415.89351806
118032.27731148
118020.128247

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
gingival epitheliumUBERON:000194993.26gold quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099191.72gold quality
islet of LangerhansUBERON:000000690.54gold quality
gingivaUBERON:000182889.85gold quality
esophagus squamous epitheliumUBERON:000692089.09gold quality
amniotic fluidUBERON:000017388.68gold quality
squamous epitheliumUBERON:000691488.60gold quality
tongue squamous epitheliumUBERON:000691988.24silver quality
palpebral conjunctivaUBERON:000181287.03gold quality
nephron tubuleUBERON:000123186.25gold quality
endothelial cellCL:000011586.06gold quality
epithelium of esophagusUBERON:000197685.76gold quality
mononuclear cellCL:000084285.44gold quality
monocyteCL:000057685.43gold quality
Brodmann (1909) area 23UBERON:001355485.30gold quality
leukocyteCL:000073885.14gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047384.97gold quality
upper leg skinUBERON:000426284.80gold quality
pancreasUBERON:000126484.48gold quality
esophagus mucosaUBERON:000246983.54gold quality
mucosa of transverse colonUBERON:000499183.54gold quality
placentaUBERON:000198783.39gold quality
cortical plateUBERON:000534383.27gold quality
skin of abdomenUBERON:000141683.03gold quality
rectumUBERON:000105282.97gold quality
metanephric glomerulusUBERON:000473682.97gold quality
lower lobe of lungUBERON:000894982.97gold quality
renal glomerulusUBERON:000007482.87gold quality
right testisUBERON:000453482.78gold quality
middle temporal gyrusUBERON:000277182.69gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3yes5.11

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

54 targeting YRDC, 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-5692A100.0074.406850
HSA-MIR-4425100.0067.591049
HSA-MIR-4789-3P99.9970.752484
HSA-MIR-477599.9875.006394
HSA-MIR-520D-5P99.9873.344883
HSA-MIR-524-5P99.9873.434882
HSA-MIR-103A-3P99.9869.141595
HSA-MIR-10799.9869.141595
HSA-MIR-302C-5P99.9772.563642
HSA-MIR-497-5P99.9271.832674
HSA-MIR-15A-5P99.9072.802787
HSA-MIR-15B-5P99.9072.782798
HSA-MIR-16-5P99.9072.802780
HSA-MIR-195-5P99.9072.812805
HSA-MIR-424-5P99.8971.902641
HSA-MIR-6838-5P99.8971.942690
HSA-MIR-3065-3P99.8770.251407
HSA-MIR-5003-3P99.8569.292517
HSA-MIR-3121-3P99.8271.963630
HSA-MIR-453099.6966.471509
HSA-MIR-46699.6770.852863
HSA-MIR-6757-3P99.6366.881089
HSA-MIR-24-3P99.5969.971934
HSA-MIR-4524A-5P99.5771.731193
HSA-MIR-4524B-5P99.5771.681195
HSA-MIR-4753-5P99.5468.511356
HSA-MIR-4708-3P99.5167.99870
HSA-MIR-365A-3P99.4370.02836
HSA-MIR-365B-3P99.4370.02836
HSA-MIR-150-3P99.4370.51920

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 86.8% of screened cell lines.

Literature-anchored findings (GeneRIF, showing 6)

  • a novel cDNA that encodes a putative human protein with yrdC domain (PMID:12730717)
  • hIRIP expression can regulate cargo assembly and function of efflux transporters, including P-glycoprotein, which mediates one of the most common mechanisms of the multidrug resistance (PMID:19279227)
  • YrdC promoted the progression of HCC. (PMID:30978526)
  • Mutations in YRDC cause an extremely severe form of Galloway-Mowat syndrome (GAMOS), an autosomal recessive disease characterized by early-onset steroid-resistant nephrotic syndrome and microcephaly. (PMID:31481669)
  • Biallelic variants in YRDC cause a developmental disorder with progeroid features. (PMID:34545459)
  • RNA Structural Dynamics Modulate EGFR-TKI Resistance Through Controlling YRDC Translation in NSCLC Cells. (PMID:36435452)

Cross-species orthologs

5 orthologs

OrganismSymbolGene ID
danio_rerioyrdcENSDARG00000041428
mus_musculusYrdcENSMUSG00000028889
rattus_norvegicusYrdcENSRNOG00000025424
drosophila_melanogasterTcs1FBGN0061361
caenorhabditis_elegansWBGENE00012997

Protein

Protein identifiers

Threonylcarbamoyl-AMP synthaseQ86U90 (reviewed: Q86U90)

Alternative names: Dopamine receptor-interacting protein 3, Ischemia/reperfusion-inducible protein homolog

All UniProt accessions (1): Q86U90

UniProt curated annotations — full annotation on UniProt →

Function. Cytoplasmic and mitochondrial threonylcarbamoyl-AMP synthase required for the formation of a threonylcarbamoyl group on adenosine at position 37 (t(6)A37) in tRNAs that read codons beginning with adenine. Catalyzes the conversion of L-threonine, HCO(3)(-)/CO(2) and ATP to give threonylcarbamoyl-AMP (TC-AMP) as the acyladenylate intermediate, with the release of diphosphate. Participates in t(6)A37 formation in cytoplasmic and mitochondrial tRNAs. May regulate the activity of some transporters.

Subunit / interactions. Interacts with RSC1A1.

Subcellular location. Cytoplasm. Mitochondrion. Cell membrane.

Tissue specificity. Ubiquitously expressed.

Disease relevance. Galloway-Mowat syndrome 10 (GAMOS10) [MIM:619609] A form of Galloway-Mowat syndrome, a severe renal-neurological disease characterized by early-onset nephrotic syndrome associated with microcephaly, central nervous system abnormalities, developmental delays, and a propensity for seizures. Brain anomalies include gyration defects ranging from lissencephaly to pachygyria and polymicrogyria, and cerebellar hypoplasia. Most patients show facial dysmorphism characterized by a small, narrow forehead, large/floppy ears, deep-set eyes, and micrognathia. Additional variable features are visual impairment and arachnodactyly. Most patients die in early childhood. GAMOS10 is an autosomal recessive form with fatal outcome. Patients manifest congenital hypothyroidism in addition to neurologic, renal and dysmorphic features. The disease is caused by variants affecting the gene represented in this entry.

Domain organisation. The mitochondrial targeting sequence (MTS) is weak and only mediates import of a small fraction of YRDC in mitochondria.

Similarity. Belongs to the SUA5 family.

RefSeq proteins (1): NP_078916* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR006070Sua5-like_domDomain
IPR017945DHBP_synth_RibB-like_a/b_domHomologous_superfamily
IPR050156TC-AMP_synthase_SUA5Family

Pfam: PF01300

Catalyzed reactions (Rhea), 1 shown:

  • L-threonine + hydrogencarbonate + ATP = L-threonylcarbamoyladenylate + diphosphate + H2O (RHEA:36407)

UniProt features (10 total): sequence variant 3, mutagenesis site 2, transit peptide 1, chain 1, domain 1, region of interest 1, modified residue 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q86U90-F183.300.69

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): 60

Mutagenesis-validated functional residues (2):

PositionPhenotype
15–17improved mitochondrial targeting sequence (mts), leading to increased import into mitochondria.
17improved mitochondrial targeting sequence (mts), leading to increased import into mitochondria.

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

IDPathway
R-HSA-6787450tRNA modification in the mitochondrion

MSigDB gene sets: 312 (showing top): HNF3ALPHA_Q6, NKX25_02, GOBP_TRNA_METABOLIC_PROCESS, LHX3_01, NAGASHIMA_NRG1_SIGNALING_UP, GARGALOVIC_RESPONSE_TO_OXIDIZED_PHOSPHOLIPIDS_BLUE_UP, CEBP_Q2, NKX62_Q2, OSWALD_HEMATOPOIETIC_STEM_CELL_IN_COLLAGEN_GEL_UP, GOBP_NEGATIVE_REGULATION_OF_TRANSPORT, SRF_C, GOBP_RNA_MODIFICATION, BRN2_01, IRF1_Q6, WTGAAAT_UNKNOWN

GO Biological Process (4): tRNA threonylcarbamoyladenosine modification (GO:0002949), regulation of translational fidelity (GO:0006450), negative regulation of transport (GO:0051051), mitochondrial tRNA modification (GO:0070900)

GO Molecular Function (6): tRNA binding (GO:0000049), double-stranded RNA binding (GO:0003725), nucleotidyltransferase activity (GO:0016779), L-threonylcarbamoyladenylate synthase activity (GO:0061710), protein binding (GO:0005515), transferase activity (GO:0016740)

GO Cellular Component (5): cytoplasm (GO:0005737), mitochondrion (GO:0005739), mitochondrial matrix (GO:0005759), plasma membrane (GO:0005886), membrane (GO:0016020)

Reactome top-level categories

Rollup of top-1 pathways:

CategoryPathways
tRNA processing1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
tRNA modification2
mitochondrion2
RNA binding2
cellular anatomical structure2
regulation of biological quality1
transport1
negative regulation of biological process1
regulation of transport1
mitochondrial tRNA processing1
mitochondrial RNA modification1
transferase activity, transferring phosphorus-containing groups1
nucleotidyltransferase activity1
binding1
catalytic activity1
intracellular anatomical structure1
cytoplasm1
intracellular membrane-bounded organelle1
intracellular organelle lumen1
membrane1
cell periphery1

Protein interactions and networks

STRING

1524 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
YRDCOSGEPL1Q9H4B0943
YRDCRBBP9O75884895
YRDCTPRKBQ9Y3C4874
YRDCQ92681Q92681873
YRDCOSGEPQ9NPF4872
YRDCLAGE3Q14657846
YRDCTP53RKQ96S44839
YRDCSLC6A2P23975774
YRDCSLC22A6Q4U2R8771
YRDCGON7Q9BXV9763
YRDCTRIT1Q9H3H1693
YRDCSLC22A2O15244686
YRDCSLC22A3O75751668
YRDCTRMT5Q32P41666
YRDCCDK5RAP1Q96SZ6560

IntAct

24 interactions, top by confidence:

ABTypeScore
DNALI1YRDCpsi-mi:“MI:0915”(physical association)0.560
BAG6YRDCpsi-mi:“MI:0915”(physical association)0.560
KLF11YRDCpsi-mi:“MI:0915”(physical association)0.560
NUP58YRDCpsi-mi:“MI:0915”(physical association)0.560
SPIN2BWDHD1psi-mi:“MI:0914”(association)0.530
SPIN1PAX3psi-mi:“MI:0914”(association)0.530
KHDRBS2SUPT5Hpsi-mi:“MI:0914”(association)0.350
FBLN5ZNF320psi-mi:“MI:0914”(association)0.350
APBA1KIF2Apsi-mi:“MI:0914”(association)0.350
NTNG1UBA6psi-mi:“MI:0914”(association)0.350
NECAP2INPPL1psi-mi:“MI:0914”(association)0.350
CALM1PLEKHG3psi-mi:“MI:0914”(association)0.350

BioGRID (36): YRDC (Affinity Capture-MS), YRDC (Affinity Capture-MS), YRDC (Biochemical Activity), YRDC (Affinity Capture-MS), YRDC (Affinity Capture-MS), YRDC (Affinity Capture-MS), YRDC (Affinity Capture-MS), YRDC (Affinity Capture-MS), YRDC (Affinity Capture-MS), YRDC (Affinity Capture-MS), YRDC (Negative Genetic), YRDC (Positive Genetic), YRDC (Affinity Capture-MS), YRDC (Affinity Capture-MS), YRDC (Affinity Capture-MS)

ESM2 similar proteins: A0JPF9, A4D126, D2GU20, E1BCH6, E9PYK3, O35465, O60888, O75425, O75808, P43896, P47823, P69678, P97812, Q0VC80, Q13144, Q14318, Q27J81, Q2VPK5, Q3B7U9, Q3TX08, Q3U269, Q496Y0, Q499R4, Q5ND52, Q5RJG7, Q5S6T3, Q64350, Q66KY3, Q6MGD0, Q6ZT62, Q7T0X7, Q7T3C3, Q86U90, Q8BGG6, Q8BYH7, Q8CHW4, Q8HXH0, Q8IYL2, Q91YR5, Q96EN8

Diamond homologs: A1S579, A5GS00, A5VFP2, A6QGV5, A7X283, A8F4E8, A8MC09, A9MHS1, O07451, P28156, P30131, P40596, P45805, P84142, Q02987, Q0VC80, Q0VTD8, Q135C2, Q13J37, Q1IKJ2, Q1MFT8, Q1QLD8, Q211P4, Q2FH34, Q2FYM9, Q2RQZ4, Q2S0V7, Q2YY14, Q3SRU5, Q3U5F4, Q43950, Q499R4, Q55638, Q58123, Q5E4P9, Q5HG16, Q5JDG7, Q5SKS6, Q6G9F7, Q6GH04

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic3
Likely pathogenic0
Uncertain significance29
Likely benign16
Benign3

Top pathogenic / likely-pathogenic (3)

Variant IDHGVSClassification
1321213NM_024640.4(YRDC):c.721_724del (p.Val241fs)Pathogenic
1321214NM_024640.4(YRDC):c.791TCC[1] (p.Leu265del)Pathogenic
1321215NM_024640.4(YRDC):c.662T>C (p.Ile221Thr)Pathogenic

SpliceAI

440 predictions. Top by Δscore:

VariantEffectΔscore
1:37803998:C:CCacceptor_gain1.0000
1:37804295:GACTT:Gdonor_loss1.0000
1:37804296:ACTT:Adonor_loss1.0000
1:37804297:CTTAC:Cdonor_loss1.0000
1:37804298:TTA:Tdonor_loss1.0000
1:37804299:TACC:Tdonor_loss1.0000
1:37804300:A:ACdonor_gain1.0000
1:37804300:ACCAG:Adonor_gain1.0000
1:37804301:C:CAdonor_loss1.0000
1:37804301:C:CGdonor_gain1.0000
1:37804301:CCAG:Cdonor_gain1.0000
1:37804301:CCAGC:Cdonor_gain1.0000
1:37804442:CTC:Cacceptor_gain1.0000
1:37804445:C:CCacceptor_gain1.0000
1:37804445:CTG:Cacceptor_loss1.0000
1:37806852:CTCA:Cdonor_loss1.0000
1:37806853:TCACC:Tdonor_loss1.0000
1:37806854:CACC:Cdonor_loss1.0000
1:37806973:CAAG:Cacceptor_gain1.0000
1:37806977:C:CCacceptor_gain1.0000
1:37807094:GACTC:Gdonor_loss1.0000
1:37807095:ACTCA:Adonor_loss1.0000
1:37807096:CTCAC:Cdonor_loss1.0000
1:37807097:TCA:Tdonor_loss1.0000
1:37807098:CA:Cdonor_loss1.0000
1:37807099:A:ACdonor_gain1.0000
1:37807099:ACAGG:Adonor_gain1.0000
1:37807100:C:CTdonor_gain1.0000
1:37807100:CA:Cdonor_gain1.0000
1:37807100:CAG:Cdonor_gain1.0000

AlphaMissense

1766 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
1:37806896:A:CS195R0.999
1:37806896:A:TS195R0.999
1:37806898:T:GS195R0.999
1:37804347:A:TV241D0.998
1:37807851:C:AK110N0.998
1:37807851:C:GK110N0.998
1:37807918:T:AD88V0.998
1:37804439:G:CF210L0.997
1:37804439:G:TF210L0.997
1:37804440:A:GF210S0.997
1:37804441:A:GF210L0.997
1:37806894:G:TA196D0.997
1:37806897:C:TS195N0.997
1:37807906:C:TG92D0.997
1:37807919:C:AD88Y0.997
1:37807919:C:GD88H0.997
1:37807927:A:TV85D0.997
1:37807930:G:TA84D0.997
1:37806897:C:AS195I0.996
1:37806906:G:TA192D0.996
1:37807113:G:CN164K0.996
1:37807113:G:TN164K0.996
1:37807820:A:GC121R0.996
1:37804322:A:CF249L0.995
1:37804322:A:TF249L0.995
1:37804324:A:GF249L0.995
1:37804410:A:TV220D0.995
1:37806890:G:CN197K0.995
1:37806890:G:TN197K0.995
1:37806903:A:GL193P0.995

dbSNP variants (sampled 300 via entrez): RS1001173441 (1:37806473 G>A,C), RS1001204513 (1:37806668 G>A), RS10015 (1:37802983 G>A), RS1002263352 (1:37805378 C>T), RS1002294536 (1:37805119 G>A), RS1003104554 (1:37808586 C>A,T), RS1003294692 (1:37803688 C>G), RS1003420581 (1:37809040 A>C,G), RS1003472677 (1:37809824 G>A,C), RS1004159505 (1:37809827 C>T), RS1004190639 (1:37810134 C>T), RS1004492793 (1:37808265 G>C,T), RS1004523861 (1:37808414 G>A), RS1004556513 (1:37808600 C>G), RS1004643690 (1:37809278 A>G)

Disease associations

OMIM: gene MIM:612276 | disease phenotypes: MIM:619609

GenCC curated gene-disease

DiseaseClassificationInheritance
Galloway-Mowat syndrome 10StrongAutosomal recessive

Mondo (1): Galloway-Mowat syndrome 10 (MONDO:0030476)

Orphanet (0):

HPO phenotypes

43 total (30 of 43 shown, HPO-id order):

HPOTerm
HP:0000007Autosomal recessive inheritance
HP:0000093Proteinuria
HP:0000100Nephrotic syndrome
HP:0000112Nephropathy
HP:0000164Abnormality of the dentition
HP:0000252Microcephaly
HP:0000316Hypertelorism
HP:0000347Micrognathia
HP:0000400Macrotia
HP:0000601Hypotelorism
HP:0000851Congenital hypothyroidism
HP:0001166Arachnodactyly
HP:0001181Adducted thumb
HP:0001250Seizure
HP:0001252Hypotonia
HP:0001263Global developmental delay
HP:0001272Cerebellar atrophy
HP:0001276Hypertonia
HP:0001302Pachygyria
HP:0001336Myoclonus
HP:0001511Intrauterine growth retardation
HP:0001622Premature birth
HP:0001967Diffuse mesangial sclerosis
HP:0002036Hiatus hernia
HP:0002059Cerebral atrophy
HP:0002188Delayed CNS myelination
HP:0002269Abnormality of neuronal migration
HP:0002353EEG abnormality
HP:0002410Aqueductal stenosis
HP:0003577Congenital onset

GWAS associations

1 associations (top):

StudyTraitp-value
GCST003476_2Eyebrow thickness7.000000e-06

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
Cyclosporineincreases expression3
sodium arseniteaffects cotreatment, decreases expression, increases expression2
Air Pollutantsincreases abundance, increases expression, decreases expression2
Estradiolaffects expression, increases expression2
Tobacco Smoke Pollutionincreases expression2
Valproic Acidaffects expression, increases expression2
Asbestos, Crocidolitedecreases expression, increases expression2
Particulate Matterincreases expression, decreases expression, increases abundance2
FR900359affects phosphorylation1
triphenyl phosphateaffects expression1
bisphenol Aaffects expression1
beta-lapachoneincreases expression1
afimoxifenedecreases reaction, increases expression1
tris(1,3-dichloro-2-propyl)phosphateincreases expression1
potassium chromate(VI)affects cotreatment, increases expression1
beta-methylcholineaffects expression1
epigallocatechin gallateaffects cotreatment, increases expression1
di-n-butylphosphoric acidaffects expression1
pentabromodiphenyl etherincreases expression1
perfluoro-n-nonanoic acidincreases expression1
monomethylarsonous acidincreases expression1
K 7174increases expression1
erucylphospho-N,N,N-trimethylpropylammoniumincreases expression1
abrineincreases expression1
2,2’,4,4’-tetrabromodiphenyl etherincreases expression1
elesclomolincreases expression1
(4-amino-1,4-dihydro-3-(2-pyridyl)-5-thioxo-1,2,4-triazole)copper(II)increases expression1
jinfukangaffects cotreatment, decreases expression1
PCI 5002affects cotreatment, increases expression1
4-(4-((5-(4,5-dimethyl-2-nitrophenyl)-2-furanyl)methylene)-4,5-dihydro-3-methyl-5-oxo-1H-pyrazol-1-yl)benzoic acidincreases expression1

Clinical trials (associated diseases)

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