PRTFDC1

gene
On this page

Also known as HHGP

Summary

PRTFDC1 (phosphoribosyl transferase domain containing 1, HGNC:23333) is a protein-coding gene on chromosome 10p12.1, encoding Phosphoribosyltransferase domain-containing protein 1 (Q9NRG1). Has low, barely detectable phosphoribosyltransferase activity (in vitro).

Enables protein homodimerization activity. Predicted to be involved in purine ribonucleoside salvage. Predicted to be active in cytosol.

Source: NCBI Gene 56952 — RefSeq curated summary.

At a glance

  • GWAS associations: 39
  • Clinical variants (ClinVar): 53 total
  • MANE Select transcript: NM_020200

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:23333
Approved symbolPRTFDC1
Namephosphoribosyl transferase domain containing 1
Location10p12.1
Locus typegene with protein product
StatusApproved
AliasesHHGP
Ensembl geneENSG00000099256
Ensembl biotypeprotein_coding
OMIM610751
Entrez56952

Gene structure

Transcript identifiers

Ensembl transcripts: 5 — 5 protein_coding

ENST00000320152, ENST00000376376, ENST00000376378, ENST00000897639, ENST00000947509

RefSeq mRNA: 2 — MANE Select: NM_020200 NM_001282786, NM_020200

CCDS: CCDS60506, CCDS7145

Canonical transcript exons

ENST00000320152 — 9 exons

ExonStartEnd
ENSE000011242452495252824952606
ENSE000013440572485138824851464
ENSE000013440612485531824855364
ENSE000013440652485691324856995
ENSE000013440692487199824872063
ENSE000013440732493718424937367
ENSE000013440782494233024942436
ENSE000016499582484861424849891
ENSE000017026502485839224858409

Expression profiles

Bgee: expression breadth ubiquitous, 240 present calls, max score 94.09.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 6.1667 / max 88.6392, expressed in 1292 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter IDTPM avgSamples expressed
1087065.94301279
2057950.127945
1087070.095854

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
corpus callosumUBERON:000233694.09gold quality
ventricular zoneUBERON:000305393.96gold quality
ganglionic eminenceUBERON:000402393.47gold quality
inferior vagus X ganglionUBERON:000536392.93gold quality
spinal cordUBERON:000224092.48gold quality
C1 segment of cervical spinal cordUBERON:000646992.30gold quality
adrenal tissueUBERON:001830391.38gold quality
medulla oblongataUBERON:000189691.02gold quality
caudate nucleusUBERON:000187390.81gold quality
putamenUBERON:000187490.80gold quality
tibiaUBERON:000097990.70gold quality
substantia nigraUBERON:000203890.60gold quality
subthalamic nucleusUBERON:000190690.57gold quality
Brodmann (1909) area 46UBERON:000648390.42gold quality
midbrainUBERON:000189190.27gold quality
amygdalaUBERON:000187690.01gold quality
nucleus accumbensUBERON:000188289.75gold quality
lateral globus pallidusUBERON:000247689.72gold quality
Ammon’s hornUBERON:000195489.49gold quality
pigmented layer of retinaUBERON:000178289.44gold quality
jejunal mucosaUBERON:000039989.33gold quality
stromal cell of endometriumCL:000225589.29gold quality
cardiac muscle of right atriumUBERON:000337989.07gold quality
superior vestibular nucleusUBERON:000722789.07gold quality
right adrenal gland cortexUBERON:003582788.96gold quality
left adrenal gland cortexUBERON:003582588.88gold quality
adrenal cortexUBERON:000123588.71gold quality
left adrenal glandUBERON:000123488.66gold quality
temporal lobeUBERON:000187188.56gold quality
right adrenal glandUBERON:000123388.53gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3yes4.69

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

45 targeting PRTFDC1, 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-574-5P100.0066.01989
HSA-MIR-7110-3P100.0073.182486
HSA-MIR-1213699.9872.815713
HSA-MIR-314899.9775.066478
HSA-MIR-548AT-5P99.9670.832666
HSA-MIR-23A-3P99.9574.243163
HSA-MIR-23B-3P99.9574.243163
HSA-MIR-23C99.9573.923192
HSA-MIR-6783-3P99.8967.922059
HSA-MIR-1343-3P99.8966.781815
HSA-MIR-576-5P99.8470.462582
HSA-MIR-3934-3P99.7665.511351
HSA-MIR-3680-3P99.7572.513095
HSA-MIR-556-3P99.7468.751203
HSA-MIR-1212499.6869.172700
HSA-MIR-129099.5969.902079
HSA-MIR-568999.5071.261154
HSA-MIR-103A-1-5P99.3967.781545
HSA-MIR-103A-2-5P99.3967.721577
HSA-MIR-446099.3768.52615
HSA-MIR-6882-5P99.3571.131206
HSA-MIR-3160-5P99.2869.071938
HSA-MIR-4667-3P99.2665.451608
HSA-MIR-4727-5P99.2367.551154
HSA-MIR-806599.1970.381289
HSA-MIR-807799.1766.67862
HSA-MIR-319999.1765.19696
HSA-MIR-805299.1765.01719
HSA-MIR-892C-5P99.1670.562116
HSA-MIR-312599.1468.492269

Literature-anchored findings (GeneRIF, showing 5)

  • epigenetic silencing of PRTFDC1 by hypermethylation of the CpG island leads to a loss of PRTFDC1 function, which might be involved in squamous cell oral carcinogenesis. (PMID:17599052)
  • The PRTFDC1 structure has been determined at 1.7 A resolution with bound GMP. The overall structure and GMP binding mode are very similar to that observed for HPRT. (PMID:21054786)
  • These results demonstrate that PRTFDC1 is a genetic modifier of HPRT-deficiency in the mouse. (PMID:21818316)
  • We found evidence for PRTFDC1 as a potential novel PTSD gene, a finding that awaits further replication. (PMID:25456346)
  • rs12411980 single-nucleotide polymorphism related to PRTFDC1 expression is significantly associated with phantom tooth pain. (PMID:39093623)

Cross-species orthologs

6 orthologs

OrganismSymbolGene ID
danio_rerioprtfdc1bENSDARG00000011683
danio_reriohprt1lENSDARG00000014866
danio_rerioprtfdc1aENSDARG00000074528
rattus_norvegicusPrtfdc1ENSRNOG00000024874
drosophila_melanogasterPgm1FBGN0003076
caenorhabditis_elegansWBGENE00019890

Paralogs (6): PGM3 (ENSG00000013375), PGM1 (ENSG00000079739), PGM5 (ENSG00000154330), PGM2L1 (ENSG00000165434), HPRT1 (ENSG00000165704), PGM2 (ENSG00000169299)

Protein

Protein identifiers

Phosphoribosyltransferase domain-containing protein 1Q9NRG1 (reviewed: Q9NRG1)

All UniProt accessions (1): Q9NRG1

UniProt curated annotations — full annotation on UniProt →

Function. Has low, barely detectable phosphoribosyltransferase activity (in vitro). Binds GMP, IMP and alpha-D-5-phosphoribosyl 1-pyrophosphate (PRPP). Is not expected to contribute to purine metabolism or GMP salvage.

Subunit / interactions. Homodimer.

Similarity. Belongs to the purine/pyrimidine phosphoribosyltransferase family.

Isoforms (3)

UniProt IDNamesCanonical?
Q9NRG1-11yes
Q9NRG1-22
Q9NRG1-33

RefSeq proteins (2): NP_001269715, NP_064585* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR000836PRTase_domDomain
IPR005904Hxn_phspho_transFamily
IPR029057PRTase-likeHomologous_superfamily
IPR050408HGPRTFamily

Pfam: PF00156

UniProt features (32 total): strand 9, helix 8, binding site 7, splice variant 2, sequence conflict 2, initiator methionine 1, chain 1, turn 1, modified residue 1

Structure

Experimental structures (PDB)

1 structures.

PDBMethodResolution (Å)
2JBHX-RAY DIFFRACTION1.7

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q9NRG1-F191.270.79

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Ligand- & substrate-binding residues (7): 141–149; 141; 142; 173; 194–195; 201; 201

Post-translational modifications (1): 2

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 90 (showing top): GSE45365_CD8A_DC_VS_CD11B_DC_IFNAR_KO_UP, GSE18804_BRAIN_VS_COLON_TUMORAL_MACROPHAGE_UP, RODRIGUES_THYROID_CARCINOMA_POORLY_DIFFERENTIATED_UP, BHATI_G2M_ARREST_BY_2METHOXYESTRADIOL_DN, GOZGIT_ESR1_TARGETS_DN, GOBP_CARBOHYDRATE_DERIVATIVE_CATABOLIC_PROCESS, GOBP_ORGANOPHOSPHATE_METABOLIC_PROCESS, GOBP_PURINE_CONTAINING_COMPOUND_SALVAGE, GOBP_CARBOHYDRATE_DERIVATIVE_METABOLIC_PROCESS, GOBP_NUCLEOBASE_CONTAINING_SMALL_MOLECULE_METABOLIC_PROCESS, GOBP_SMALL_MOLECULE_BIOSYNTHETIC_PROCESS, GOBP_NUCLEOBASE_METABOLIC_PROCESS, GOBP_CARBOHYDRATE_DERIVATIVE_BIOSYNTHETIC_PROCESS, GOBP_PURINE_NUCLEOBASE_BIOSYNTHETIC_PROCESS, GOBP_NUCLEOSIDE_SALVAGE

GO Biological Process (1): purine ribonucleoside salvage (GO:0006166)

GO Molecular Function (6): nucleotide binding (GO:0000166), magnesium ion binding (GO:0000287), protein homodimerization activity (GO:0042803), hypoxanthine phosphoribosyltransferase activity (GO:0004422), protein binding (GO:0005515), metal ion binding (GO:0046872)

GO Cellular Component (1): cytosol (GO:0005829)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
purine-containing compound salvage1
nucleoside salvage1
purine ribonucleoside biosynthetic process1
nucleoside phosphate binding1
heterocyclic compound binding1
metal ion binding1
identical protein binding1
protein dimerization activity1
purine phosphoribosyltransferase activity1
binding1
cation binding1
cytoplasm1
cellular anatomical structure1

Protein interactions and networks

STRING

1615 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
PRTFDC1APRTP07741608
PRTFDC1ANKRD55Q3KP44570
PRTFDC1TLL1O43897542
PRTFDC1RNASE1P07998542
PRTFDC1ZNF626Q68DY1487
PRTFDC1GARTP22102445
PRTFDC1COBLO75128436
PRTFDC1PPP1R14CQ8TAE6433
PRTFDC1TIPE1Q8WVP5428
PRTFDC1EN2P19622425
PRTFDC1UMPSP11172423
PRTFDC1GMPSP49915419
PRTFDC1TK2O00142410
PRTFDC1ZNF709Q8N972388
PRTFDC1ADSS2P30520387

IntAct

93 interactions, top by confidence:

ABTypeScore
HPRT1PRTFDC1psi-mi:“MI:0915”(physical association)0.920
PRTFDC1HPRT1psi-mi:“MI:0915”(physical association)0.920
EEF2KMTPRTFDC1psi-mi:“MI:0915”(physical association)0.830
PRTFDC1EEF2KMTpsi-mi:“MI:0915”(physical association)0.830
PRTFDC1TCL1Apsi-mi:“MI:0915”(physical association)0.720
PRTFDC1EPM2AIP1psi-mi:“MI:0915”(physical association)0.720
TCL1APRTFDC1psi-mi:“MI:0915”(physical association)0.720
EPM2AIP1PRTFDC1psi-mi:“MI:0915”(physical association)0.720
MCMBPPRTFDC1psi-mi:“MI:0915”(physical association)0.720
PRTFDC1GNPDA1psi-mi:“MI:0915”(physical association)0.560
PRTFDC1LGALS9Bpsi-mi:“MI:0915”(physical association)0.560

BioGRID (65): PRTFDC1 (Two-hybrid), PRTFDC1 (Two-hybrid), PRTFDC1 (Two-hybrid), PRTFDC1 (Two-hybrid), MCMBP (Two-hybrid), EEF2KMT (Two-hybrid), LGALS9B (Two-hybrid), PRTFDC1 (Affinity Capture-MS), PRTFDC1 (Affinity Capture-MS), PRTFDC1 (Affinity Capture-MS), PRTFDC1 (Affinity Capture-MS), PRTFDC1 (Affinity Capture-MS), PRTFDC1 (Affinity Capture-MS), PRTFDC1 (Two-hybrid), NIF3L1 (Two-hybrid)

ESM2 similar proteins: A4II60, A5A6I1, B4S3A5, G5EDZ2, O42895, O65583, O74427, O94710, P00492, P00493, P00494, P07833, P09383, P20035, P27515, P27605, P41888, P43152, P47959, P56523, Q07010, Q10439, Q1RMS2, Q25566, Q26997, Q26998, Q27541, Q2M197, Q3SZ18, Q45FY6, Q55EL3, Q5F3Z1, Q64531, Q6DCP3, Q6GQ37, Q6LDD9, Q6LZE9, Q6WIT9, Q8VYB2, Q9FKS0

Diamond homologs: A4II60, A5A6I1, C0ZG45, O66821, O69537, P00492, P00493, P00494, P07833, P09383, P0A5T1, P0A9M2, P0A9M3, P0A9M4, P18134, P20035, P27605, P37171, P37472, P43152, P45078, P47959, P51900, P71479, P96794, P9WHQ8, P9WHQ9, Q02522, Q26997, Q3SZ18, Q45FY6, Q5HRP4, Q64531, Q6DCP3, Q6LDD9, Q6WIT9, Q724J4, Q839B2, Q8CQV4, Q8DRP8

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance38
Likely benign1
Benign1

Top pathogenic / likely-pathogenic (0)

SpliceAI

2097 predictions. Top by Δscore:

VariantEffectΔscore
10:24855316:A:ACdonor_gain1.0000
10:24855317:C:CCdonor_gain1.0000
10:24855317:CAGT:Cdonor_gain1.0000
10:24856995:CCTT:Cacceptor_gain1.0000
10:24872062:TT:Tacceptor_gain1.0000
10:24872064:C:CCacceptor_gain1.0000
10:24937179:CTT:Cdonor_loss1.0000
10:24937180:TTA:Tdonor_loss1.0000
10:24937181:TAC:Tdonor_loss1.0000
10:24937182:A:ACdonor_gain1.0000
10:24937182:A:Tdonor_loss1.0000
10:24937182:AC:Adonor_gain1.0000
10:24937182:ACC:Adonor_gain1.0000
10:24937183:C:CCdonor_gain1.0000
10:24937183:CC:Cdonor_gain1.0000
10:24937183:CCC:Cdonor_gain1.0000
10:24937183:CCCT:Cdonor_gain1.0000
10:24937363:CAATT:Cacceptor_gain1.0000
10:24937364:AATT:Aacceptor_gain1.0000
10:24937365:ATT:Aacceptor_gain1.0000
10:24937365:ATTC:Aacceptor_loss1.0000
10:24937366:TT:Tacceptor_gain1.0000
10:24937366:TTC:Tacceptor_loss1.0000
10:24937367:TC:Tacceptor_loss1.0000
10:24937368:C:Aacceptor_loss1.0000
10:24937368:C:CCacceptor_gain1.0000
10:24937369:T:Cacceptor_loss1.0000
10:24851386:A:ACdonor_gain0.9900
10:24851387:C:CCdonor_gain0.9900
10:24851466:T:Cacceptor_gain0.9900

AlphaMissense

1494 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
10:24937205:G:CF106L0.996
10:24937205:G:TF106L0.996
10:24937207:A:GF106L0.996
10:24851428:C:TG197E0.995
10:24851454:A:CF188L0.994
10:24851454:A:TF188L0.994
10:24851456:A:GF188L0.994
10:24851429:C:GG197R0.993
10:24851429:C:TG197R0.993
10:24851436:A:CF194L0.992
10:24851436:A:TF194L0.992
10:24851438:A:GF194L0.992
10:24937269:A:GL85P0.992
10:24851455:A:GF188S0.991
10:24858396:A:TV140D0.991
10:24849887:A:TI212K0.990
10:24851397:T:AR207S0.990
10:24851397:T:GR207S0.990
10:24851398:C:AR207I0.990
10:24851398:C:GR207T0.990
10:24851428:C:AG197V0.990
10:24855364:A:CS169R0.990
10:24855364:A:TS169R0.990
10:24856914:T:GS169R0.990
10:24858405:A:TV137D0.990
10:24937280:G:CF81L0.990
10:24937280:G:TF81L0.990
10:24937282:A:GF81L0.990
10:24937367:T:AR52S0.990
10:24937367:T:GR52S0.990

dbSNP variants (sampled 300 via entrez): RS1000007917 (10:24860416 C>T), RS1000087551 (10:24905072 C>T), RS1000092291 (10:24947201 C>A), RS1000114115 (10:24860971 T>C), RS1000117714 (10:24930744 C>T), RS1000159606 (10:24924896 G>A), RS1000177208 (10:24864293 G>T), RS1000236050 (10:24919180 A>C), RS1000280763 (10:24878054 G>A,T), RS1000368065 (10:24872725 A>T), RS1000372842 (10:24889993 G>C), RS1000419708 (10:24912605 T>C), RS1000426543 (10:24947640 T>C), RS1000433011 (10:24954587 C>A,G), RS1000434166 (10:24851865 C>G,T)

Disease associations

OMIM: gene MIM:610751 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

39 associations (top):

StudyTraitp-value
GCST001762_334Obesity-related traits3.000000e-06
GCST002118_1Metabolite levels (Pyroglutamine)4.000000e-06
GCST002681_1Post-traumatic stress disorder2.000000e-09
GCST002875_1Diisocyanate-induced asthma5.000000e-06
GCST004603_50Platelet count4.000000e-10
GCST004607_114Plateletcrit7.000000e-13
GCST004610_108White blood cell count1.000000e-44
GCST004611_50High light scatter reticulocyte count1.000000e-205
GCST004612_106High light scatter reticulocyte percentage of red cells6.000000e-202
GCST004613_14Sum neutrophil eosinophil counts3.000000e-32
GCST004614_35Granulocyte count2.000000e-32
GCST004619_203Reticulocyte fraction of red cells8.000000e-163
GCST004620_113Sum basophil neutrophil counts3.000000e-32
GCST004621_12Red cell distribution width6.000000e-16
GCST004622_29Reticulocyte count2.000000e-163
GCST004625_176Monocyte count8.000000e-48
GCST004626_76Myeloid white cell count3.000000e-39
GCST004627_7Lymphocyte count9.000000e-17
GCST004628_108Immature fraction of reticulocytes4.000000e-139
GCST004629_87Neutrophil count2.000000e-32
GCST005580_102Intraocular pressure4.000000e-08
GCST005580_185Intraocular pressure2.000000e-08
GCST008764_3Perceived intensity of neohesperidin dihydrochalcone8.000000e-06
GCST90000025_394Appendicular lean mass3.000000e-40
GCST90002381_320Eosinophil count1.000000e-14
GCST90002385_473High light scatter reticulocyte count0.000000e+00
GCST90002386_394High light scatter reticulocyte percentage of red cells0.000000e+00
GCST90002387_350Immature fraction of reticulocytes1.000000e-308
GCST90002388_550Lymphocyte count1.000000e-47
GCST90002393_326Monocyte count1.000000e-95

EFO canonical traits (17, from GWAS)

EFO IDTrait name
EFO:0005106body composition measurement
EFO:0005408pyroglutamine measurement
EFO:0006995response to diisocyanate
EFO:0004309platelet count
EFO:0007985platelet crit
EFO:0007986reticulocyte count
EFO:0004833neutrophil count
EFO:0004842eosinophil count
EFO:0007987granulocyte count
EFO:0005090basophil count
EFO:0009188Red cell distribution width
EFO:0005091monocyte count
EFO:0004587lymphocyte count
EFO:0004695intraocular pressure measurement
EFO:0004980appendicular lean mass
EFO:0007984platelet component distribution width
EFO:0007789BMI-adjusted waist circumference

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
Valproic Acidaffects cotreatment, increases expression, affects expression4
bisphenol Aaffects cotreatment, increases methylation, decreases expression3
arseniteaffects binding, increases reaction, increases methylation2
sodium arseniteaffects acetylation, affects methylation, increases expression2
(+)-JQ1 compounddecreases expression2
Air Pollutantsdecreases expression, increases abundance, increases expression2
Particulate Matterdecreases expression, increases abundance, increases expression2
aristolochic acid Idecreases expression, increases expression1
methylmercuric chloridedecreases expression1
triphenyl phosphateaffects expression1
glycidyl methacrylatedecreases expression1
methylparabendecreases expression1
CGP 52608affects binding, increases reaction1
monomethylarsonous acidaffects methylation, affects acetylation1
abrinedecreases expression1
bisphenol Sincreases methylation1
jinfukangdecreases expression1
Temozolomidedecreases expression1
Decitabineaffects methylation1
Sunitinibdecreases expression1
Zoledronic Aciddecreases expression1
Fulvestrantincreases methylation, affects cotreatment1
Arsenicaffects methylation1
Vehicle Emissionsincreases abundance, increases expression1
Benzo(a)pyreneaffects methylation1
Doxorubicindecreases expression1
Flame Retardantsdecreases expression1
Hydralazineaffects cotreatment, increases expression1
Ivermectindecreases expression1
Methyl Methanesulfonatedecreases expression1

Clinical trials (associated diseases)

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

  • Disease cohort memberships (association, not causation — diseases whose associated-gene cohort lists this gene; a subset are also under Associated diseases): post-traumatic stress disorder