KEGG   VARIANT: 7428v3
Entry
7428v3                      Variant                                
Name
VHL mutation
Gene
VHL  von Hippel-Lindau tumor suppressor [KO:K03871]
Organism
hsa_var Human gene variants (Homo sapiens)
Variation
mutations
OmimVar: 608537
Reference
PMID:8956040
  Authors
Zbar B, Kishida T, Chen F, Schmidt L, Maher ER, Richards FM, Crossey PA, Webster AR, Affara NA, Ferguson-Smith MA, Brauch H, Glavac D, Neumann HP, Tisherman S, Mulvihill JJ, Gross DJ, Shuin T, Whaley J, Seizinger B, Kley N, Olschwang S, Boisson C, Richard S, Lips CH, Lerman M, et al.
  Title
Germline mutations in the Von Hippel-Lindau disease (VHL) gene in families from North America, Europe, and Japan.
  Journal
Hum Mutat 8:348-57 (1996)
DOI:10.1002/(SICI)1098-1004(1996)8:4<348::AID-HUMU8>3.0.CO;2-3
Reference
PMID:11986208
  Authors
Wiesener MS, Seyfarth M, Warnecke C, Jurgensen JS, Rosenberger C, Morgan NV, Maher ER, Frei U, Eckardt KU
  Title
Paraneoplastic erythrocytosis associated with an inactivating point mutation of the von Hippel-Lindau gene in a renal cell carcinoma.
  Journal
Blood 99:3562-5 (2002)
DOI:10.1182/blood.v99.10.3562
Reference
PMID:17992257
  Authors
Hickey MM, Lam JC, Bezman NA, Rathmell WK, Simon MC
  Title
von Hippel-Lindau mutation in mice recapitulates Chuvash polycythemia via hypoxia-inducible factor-2alpha signaling and splenic erythropoiesis.
  Journal
J Clin Invest 117:3879-89 (2007)
DOI:10.1172/JCI32614
LinkDB

KEGG   Homo sapiens (human): 9978
Entry
9978              CDS       T01001                                 
Symbol
RBX1, BA554C12.1, RNF75, ROC1
Name
(RefSeq) ring-box 1
  KO
K03868  E3 ubiquitin-protein ligase RBX1 [EC:2.3.2.32]
Organism
hsa  Homo sapiens (human)
Pathway
hsa03420  Nucleotide excision repair
hsa04066  HIF-1 signaling pathway
hsa04110  Cell cycle
hsa04114  Oocyte meiosis
hsa04120  Ubiquitin mediated proteolysis
hsa04141  Protein processing in endoplasmic reticulum
hsa04310  Wnt signaling pathway
hsa04350  TGF-beta signaling pathway
hsa04710  Circadian rhythm
hsa05131  Shigellosis
hsa05170  Human immunodeficiency virus 1 infection
hsa05200  Pathways in cancer
hsa05211  Renal cell carcinoma
Network
nt06165  Epstein-Barr virus (EBV)
nt06166  Human papillomavirus (HPV)
nt06182  Shigella
nt06225  HIF-1 signaling (cancer)
nt06230  Cell cycle (cancer)
nt06261  Gastric cancer
nt06264  Renal cell carcinoma
nt06267  Small cell lung cancer
nt06272  Prostate cancer
nt06502  Nucleotide excision repair
nt06509  DNA replication
nt06516  TNF signaling
nt06541  Cytoskeleton in neurons
nt06542  HIF signaling
  Element
N00080  Loss of VHL to HIF-1 signaling pathway
N00081  Mutation-inactivated VHL to HIF-1 signaling pathway
N00091  p27-Cell cycle G1/S
N00092  Amplified MYC to p27-cell cycle G1/S
N00942  Shigella OspG to TNF-NFKB signaling pathway
N01425  Global genome NER
N01430  Transcription-coupled NER
N01473  DNA replication termination
N01855  Neurofilament regulation, ubiqutination by Gigaxonin
N01872  Proteasomal degradation of HIF by VHL complex
N01873  VHL mutation to HIF-2 signaling pathway
Brite
KEGG Orthology (KO) [BR:hsa00001]
 09120 Genetic Information Processing
  09123 Folding, sorting and degradation
   04141 Protein processing in endoplasmic reticulum
    9978 (RBX1)
   04120 Ubiquitin mediated proteolysis
    9978 (RBX1)
  09124 Replication and repair
   03420 Nucleotide excision repair
    9978 (RBX1)
 09130 Environmental Information Processing
  09132 Signal transduction
   04310 Wnt signaling pathway
    9978 (RBX1)
   04350 TGF-beta signaling pathway
    9978 (RBX1)
   04066 HIF-1 signaling pathway
    9978 (RBX1)
 09140 Cellular Processes
  09143 Cell growth and death
   04110 Cell cycle
    9978 (RBX1)
   04114 Oocyte meiosis
    9978 (RBX1)
 09150 Organismal Systems
  09159 Environmental adaptation
   04710 Circadian rhythm
    9978 (RBX1)
 09160 Human Diseases
  09161 Cancer: overview
   05200 Pathways in cancer
    9978 (RBX1)
  09162 Cancer: specific types
   05211 Renal cell carcinoma
    9978 (RBX1)
  09172 Infectious disease: viral
   05170 Human immunodeficiency virus 1 infection
    9978 (RBX1)
  09171 Infectious disease: bacterial
   05131 Shigellosis
    9978 (RBX1)
 09180 Brite Hierarchies
  09182 Protein families: genetic information processing
   04121 Ubiquitin system [BR:hsa04121]
    9978 (RBX1)
   03400 DNA repair and recombination proteins [BR:hsa03400]
    9978 (RBX1)
Enzymes [BR:hsa01000]
 2. Transferases
  2.3  Acyltransferases
   2.3.2  Aminoacyltransferases
    2.3.2.32  cullin-RING-type E3 NEDD8 transferase
     9978 (RBX1)
Ubiquitin system [BR:hsa04121]
 Ubiquitin ligases (E3)
  UBL E3 ligases
   9978 (RBX1)
  Multi subunit type E3
   SCF complex
    Ring finger protein
     9978 (RBX1)
   Cul2 complex
     9978 (RBX1)
   Cul3 complex
     9978 (RBX1)
   Cul4 complex
     9978 (RBX1)
   Cul7 complex
     9978 (RBX1)
   Cul8 complex
     9978 (RBX1)
   Cul9 complex
     9978 (RBX1)
DNA repair and recombination proteins [BR:hsa03400]
 Eukaryotic type
  SSBR (single strand breaks repair)
   NER (nucleotide excision repair)
    GGR (global genome repair) factors
     Cul4-DDB2 complex
      9978 (RBX1)
    TCR (transcription coupled repair) factors
     Cul4-CSA complex
      9978 (RBX1)
SSDB
Motif
Pfam: zf-rbx1 zf-ANAPC11 zf-RING_2 zf-C3HC4 zf-C3HC4_2 zf-RING_11 DUF8003 PHD_NSD
Other DBs
NCBI-GeneID: 9978
NCBI-ProteinID: NP_055063
OMIM: 603814
HGNC: 9928
Ensembl: ENSG00000100387
UniProt: P62877
Structure
LinkDB
Position
22:40951378..40973309
AA seq 108 aa
MAAAMDVDTPSGTNSGAGKKRFEVKKWNAVALWAWDIVVDNCAICRNHIMDLCIECQANQ
ASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLDNREWEFQKYGH
NT seq 327 nt   +upstreamnt  +downstreamnt
atggcggcagcgatggatgtggataccccgagcggcaccaacagcggcgcgggcaagaag
cgctttgaagtgaaaaagtggaatgcagtagccctctgggcctgggatattgtggttgat
aactgtgccatctgcaggaaccacattatggatctttgcatagaatgtcaagctaaccag
gcgtccgctacttcagaagagtgtactgtcgcatggggagtctgtaaccatgcttttcac
ttccactgcatctctcgctggctcaaaacacgacaggtgtgtccattggacaacagagag
tgggaattccaaaagtatgggcactag

KEGG   Homo sapiens (human): 6921
Entry
6921              CDS       T01001                                 
Symbol
ELOC, SIII, TCEB1
Name
(RefSeq) elongin C
  KO
K03872  elongin-C
Organism
hsa  Homo sapiens (human)
Pathway
hsa04066  HIF-1 signaling pathway
hsa04120  Ubiquitin mediated proteolysis
hsa05170  Human immunodeficiency virus 1 infection
hsa05200  Pathways in cancer
hsa05211  Renal cell carcinoma
Network
nt06225  HIF-1 signaling (cancer)
nt06264  Renal cell carcinoma
nt06509  DNA replication
nt06523  Epigenetic regulation by Polycomb complexes
nt06542  HIF signaling
  Element
N00080  Loss of VHL to HIF-1 signaling pathway
N00081  Mutation-inactivated VHL to HIF-1 signaling pathway
N01473  DNA replication termination
N01577  Gene silencing by methylation of H3K27 and ubiquitination of H2AK119
N01872  Proteasomal degradation of HIF by VHL complex
N01873  VHL mutation to HIF-2 signaling pathway
Brite
KEGG Orthology (KO) [BR:hsa00001]
 09120 Genetic Information Processing
  09123 Folding, sorting and degradation
   04120 Ubiquitin mediated proteolysis
    6921 (ELOC)
 09130 Environmental Information Processing
  09132 Signal transduction
   04066 HIF-1 signaling pathway
    6921 (ELOC)
 09160 Human Diseases
  09161 Cancer: overview
   05200 Pathways in cancer
    6921 (ELOC)
  09162 Cancer: specific types
   05211 Renal cell carcinoma
    6921 (ELOC)
  09172 Infectious disease: viral
   05170 Human immunodeficiency virus 1 infection
    6921 (ELOC)
 09180 Brite Hierarchies
  09182 Protein families: genetic information processing
   04121 Ubiquitin system [BR:hsa04121]
    6921 (ELOC)
   03400 DNA repair and recombination proteins [BR:hsa03400]
    6921 (ELOC)
Ubiquitin system [BR:hsa04121]
 Ubiquitin ligases (E3)
  Multi subunit type E3
   Cul2 complex
    Adoptor protein
     6921 (ELOC)
   Cul5 complex
     6921 (ELOC)
DNA repair and recombination proteins [BR:hsa03400]
 Eukaryotic type
  SSBR (single strand breaks repair)
   NER (nucleotide excision repair)
    Other NER factors
     6921 (ELOC)
SSDB
Motif
Pfam: Skp1_POZ
Other DBs
NCBI-GeneID: 6921
NCBI-ProteinID: NP_001191786
OMIM: 600788
HGNC: 11617
Ensembl: ENSG00000154582
UniProt: Q15369
Structure
LinkDB
Position
8:complement(73945119..73972287)
AA seq 112 aa
MDGEEKTYGGCEGPDAMYVKLISSDGHEFIVKREHALTSGTIKAMLSGPGQFAENETNEV
NFREIPSHVLSKVCMYFTYKVRYTNSSTEIPEFPIAPEIALELLMAANFLDC
NT seq 339 nt   +upstreamnt  +downstreamnt
atggatggagaggagaaaacctatggtggctgtgaaggacctgatgccatgtatgtcaaa
ttgatatcatctgatggccatgaatttattgtaaaaagagaacatgcattaacatcaggc
acgataaaagccatgttgagtggcccaggtcagtttgctgagaacgaaaccaatgaggtc
aattttagagagataccttcacatgtgctatcgaaagtatgcatgtattttacgtacaag
gttcgctacactaacagctccaccgagattcctgaattcccaattgcacctgaaattgca
ctggaactgctgatggctgcgaacttcttagattgttaa

KEGG   Homo sapiens (human): 6923
Entry
6923              CDS       T01001                                 
Symbol
ELOB, SIII, TCEB2
Name
(RefSeq) elongin B
  KO
K03873  elongin-B
Organism
hsa  Homo sapiens (human)
Pathway
hsa04066  HIF-1 signaling pathway
hsa04120  Ubiquitin mediated proteolysis
hsa05170  Human immunodeficiency virus 1 infection
hsa05200  Pathways in cancer
hsa05211  Renal cell carcinoma
Network
nt06225  HIF-1 signaling (cancer)
nt06264  Renal cell carcinoma
nt06509  DNA replication
nt06523  Epigenetic regulation by Polycomb complexes
nt06542  HIF signaling
  Element
N00080  Loss of VHL to HIF-1 signaling pathway
N00081  Mutation-inactivated VHL to HIF-1 signaling pathway
N01473  DNA replication termination
N01577  Gene silencing by methylation of H3K27 and ubiquitination of H2AK119
N01872  Proteasomal degradation of HIF by VHL complex
N01873  VHL mutation to HIF-2 signaling pathway
Brite
KEGG Orthology (KO) [BR:hsa00001]
 09120 Genetic Information Processing
  09123 Folding, sorting and degradation
   04120 Ubiquitin mediated proteolysis
    6923 (ELOB)
 09130 Environmental Information Processing
  09132 Signal transduction
   04066 HIF-1 signaling pathway
    6923 (ELOB)
 09160 Human Diseases
  09161 Cancer: overview
   05200 Pathways in cancer
    6923 (ELOB)
  09162 Cancer: specific types
   05211 Renal cell carcinoma
    6923 (ELOB)
  09172 Infectious disease: viral
   05170 Human immunodeficiency virus 1 infection
    6923 (ELOB)
 09180 Brite Hierarchies
  09182 Protein families: genetic information processing
   04121 Ubiquitin system [BR:hsa04121]
    6923 (ELOB)
   03400 DNA repair and recombination proteins [BR:hsa03400]
    6923 (ELOB)
Ubiquitin system [BR:hsa04121]
 Ubiquitin ligases (E3)
  Multi subunit type E3
   Cul2 complex
    Adoptor protein
     6923 (ELOB)
   Cul5 complex
     6923 (ELOB)
DNA repair and recombination proteins [BR:hsa03400]
 Eukaryotic type
  SSBR (single strand breaks repair)
   NER (nucleotide excision repair)
    Other NER factors
     6923 (ELOB)
SSDB
Motif
Pfam: ubiquitin Rad60-SLD
Other DBs
NCBI-GeneID: 6923
NCBI-ProteinID: NP_009039
OMIM: 600787
HGNC: 11619
Ensembl: ENSG00000103363
UniProt: Q15370
Structure
LinkDB
Position
16:complement(2771414..2777280)
AA seq 118 aa
MDVFLMIRRHKTTIFTDAKESSTVFELKRIVEGILKRPPDEQRLYKDDQLLDDGKTLGEC
GFTSQTARPQAPATVGLAFRADDTFEALCIEPFSSPPELPDVMKPQDSGSSANEQAVQ
NT seq 357 nt   +upstreamnt  +downstreamnt
atggacgtgttcctcatgatccggcgccacaagaccaccatcttcacggacgccaaggag
tccagcacggtgttcgaactgaagcgcatcgtcgagggcatcctcaagcggcctcctgac
gagcagcggctgtacaaggatgaccaactcttggatgatggcaagacactgggcgagtgt
ggcttcaccagtcaaacagcacggccacaggccccagccacagtggggctggccttccgg
gcagatgacacctttgaggccctgtgcatcgagccgttttccagcccgccagagctgccc
gatgtgatgaagccccaggactcgggaagcagtgccaatgaacaagccgtgcagtga

KEGG   Homo sapiens (human): 8453
Entry
8453              CDS       T01001                                 
Symbol
CUL2
Name
(RefSeq) cullin 2
  KO
K03870  cullin 2
Organism
hsa  Homo sapiens (human)
Pathway
hsa04066  HIF-1 signaling pathway
hsa04120  Ubiquitin mediated proteolysis
hsa05200  Pathways in cancer
hsa05211  Renal cell carcinoma
Network
nt06225  HIF-1 signaling (cancer)
nt06264  Renal cell carcinoma
nt06509  DNA replication
nt06542  HIF signaling
  Element
N00080  Loss of VHL to HIF-1 signaling pathway
N00081  Mutation-inactivated VHL to HIF-1 signaling pathway
N01473  DNA replication termination
N01872  Proteasomal degradation of HIF by VHL complex
N01873  VHL mutation to HIF-2 signaling pathway
Brite
KEGG Orthology (KO) [BR:hsa00001]
 09120 Genetic Information Processing
  09123 Folding, sorting and degradation
   04120 Ubiquitin mediated proteolysis
    8453 (CUL2)
 09130 Environmental Information Processing
  09132 Signal transduction
   04066 HIF-1 signaling pathway
    8453 (CUL2)
 09160 Human Diseases
  09161 Cancer: overview
   05200 Pathways in cancer
    8453 (CUL2)
  09162 Cancer: specific types
   05211 Renal cell carcinoma
    8453 (CUL2)
 09180 Brite Hierarchies
  09182 Protein families: genetic information processing
   04121 Ubiquitin system [BR:hsa04121]
    8453 (CUL2)
Ubiquitin system [BR:hsa04121]
 Ubiquitin ligases (E3)
  Multi subunit type E3
   Cul2 complex
    Cullin
     8453 (CUL2)
SSDB
Motif
Pfam: Cullin Cullin_AB Cullin_Nedd8 Rio2_N DUF4423 TFIIE_alpha
Other DBs
NCBI-GeneID: 8453
NCBI-ProteinID: NP_001185706
OMIM: 603135
HGNC: 2552
Ensembl: ENSG00000108094
UniProt: Q13617 A0A140VKB1
Structure
LinkDB
Position
10:complement(35008551..35127006)
AA seq 745 aa
MSLKPRVVDFDETWNKLLTTIKAVVMLEYVERATWNDRFSDIYALCVAYPEPLGERLYTE
TKIFLENHVRHLHKRVLESEEQVLVMYHRYWEEYSKGADYMDCLYRYLNTQFIKKNKLTE
ADLQYGYGGVDMNEPLMEIGELALDMWRKLMVEPLQAILIRMLLREIKNDRGGEDPNQKV
IHGVINSFVHVEQYKKKFPLKFYQEIFESPFLTETGEYYKQEASNLLQESNCSQYMEKVL
GRLKDEEIRCRKYLHPSSYTKVIHECQQRMVADHLQFLHAECHNIIRQEKKNDMANMYVL
LRAVSTGLPHMIQELQNHIHDEGLRATSNLTQENMPTLFVESVLEVHGKFVQLINTVLNG
DQHFMSALDKALTSVVNYREPKSVCKAPELLAKYCDNLLKKSAKGMTENEVEDRLTSFIT
VFKYIDDKDVFQKFYARMLAKRLIHGLSMSMDSEEAMINKLKQACGYEFTSKLHRMYTDM
SVSADLNNKFNNFIKNQDTVIDLGISFQIYVLQAGAWPLTQAPSSTFAIPQELEKSVQMF
ELFYSQHFSGRKLTWLHYLCTGEVKMNYLGKPYVAMVTTYQMAVLLAFNNSETVSYKELQ
DSTQMNEKELTKTIKSLLDVKMINHDSEKEDIDAESSFSLNMNFSSKRTKFKITTSMQKD
TPQEMEQTRSAVDEDRKMYLQAAIVRIMKARKVLRHNALIQEVISQSRARFNPSISMIKK
CIEVLIDKQYIERSQASADEYSYVA
NT seq 2238 nt   +upstreamnt  +downstreamnt
atgtctttgaaaccaagagtagtagattttgatgaaacatggaacaaacttttgacgaca
ataaaagccgtggtcatgttggaatacgtcgaaagagcaacatggaatgaccgtttctca
gatatctatgctttatgtgtggcctatcctgaaccccttggagaaagactttatacagaa
actaagatttttttggaaaatcatgttcggcatttgcataagagagttttggagtcagaa
gaacaagtacttgttatgtatcataggtactgggaagaatacagcaagggtgcagactat
atggactgcttatataggtatctcaacacccagtttattaaaaagaataaattaacagaa
gcggaccttcagtatggctatggtggtgtagatatgaatgaaccacttatggaaatagga
gagctagcattggatatgtggaggaaattgatggttgaaccacttcaggccatccttatc
cgaatgctgctccgagaaatcaaaaatgatcgtggtggagaagacccaaaccagaaagta
atccatggggttattaactcctttgttcatgttgaacagtataagaaaaaattcccctta
aagttttatcaggaaatttttgagtctccctttctgactgaaacaggagagtattacaaa
caagaagcttcaaatttattacaagaatcaaactgctcacagtatatggaaaaggttcta
ggtagattaaaagatgaagaaattcgatgtcgaaaatacctacatccaagttcatatact
aaggtgattcatgaatgtcaacaacgaatggtagcagaccacttacagtttttacatgca
gaatgtcataatataattcgacaagagaaaaaaaatgacatggcaaatatgtacgtctta
ctccgtgctgtgtccactggtttacctcatatgattcaggagctgcaaaaccacatccat
gatgagggccttcgagcaaccagcaaccttactcaggaaaacatgccaacactatttgtg
gagtcagttttggaagtgcatggtaaatttgttcagcttatcaacactgttttgaatggt
gatcagcattttatgagtgcgttggataaggcccttacgtcagttgtaaattacagagaa
cctaagtctgtttgcaaagcacctgaactgcttgctaagtactgtgacaacttactgaag
aagtcagcgaaagggatgacagagaatgaagtggaagacaggctcacgagcttcatcaca
gtgttcaaatacattgatgacaaggacgtctttcaaaagttctacgcaagaatgctggca
aaacgtttaattcatgggttatccatgtctatggactctgaagaagccatgatcaacaaa
ttaaagcaagcctgtggttatgagtttaccagcaagctacatcggatgtatacagatatg
agtgtcagcgctgatctcaacaataagttcaacaattttatcaaaaaccaagacacagta
atagatttgggaattagttttcaaatatatgttctacaggctggtgcgtggcctcttact
caggctccttcatctacgtttgcaattccccaggaattagaaaaaagtgtacagatgttt
gaattattttatagccaacatttcagtggaaggaaacttacatggttacattatctgtgt
acaggtgaagttaaaatgaactatttgggcaaaccatatgtagccatggttacaacatac
caaatggcagttcttcttgcctttaacaacagtgaaactgtcagttataaagagcttcag
gacagcactcagatgaatgaaaaggaactgacaaaaacaatcaaatcattacttgatgtg
aaaatgattaaccatgattcagaaaaggaagatattgatgcagaatcttcgttttcatta
aatatgaactttagcagtaaaagaacaaaatttaaaattactacatcaatgcagaaagac
acaccacaagaaatggagcagactagaagtgcagttgatgaggaccggaaaatgtatctc
caagctgctatagttcgtatcatgaaagcacgaaaagtgcttcggcacaatgcccttatt
caagaggtgattagccagtcaagagctaggtttaatcccagtatcagcatgattaagaag
tgtattgaagttctgatagacaaacaatacatagaacgcagccaggcgtcggcagatgaa
tacagctacgtcgcgtga

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