LOCUS       NM_006214               1541 bp    mRNA    linear   PRI 09-OCT-2024
DEFINITION  Homo sapiens phytanoyl-CoA 2-hydroxylase (PHYH), transcript variant
            1, mRNA.
ACCESSION   NM_006214
VERSION     NM_006214.4
KEYWORDS    RefSeq; MANE Select.
SOURCE      Homo sapiens (human)
  ORGANISM  Homo sapiens
            Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
            Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini;
            Catarrhini; Hominidae; Homo.
REFERENCE   1  (bases 1 to 1541)
  AUTHORS   Daich Varela,M., Schiff,E., Malka,S., Wright,G., Mahroo,O.A.,
            Webster,A.R., Michaelides,M. and Arno,G.
  TITLE     PHYH c.678+5G>T Leads to In-Frame Exon Skipping and Is Associated
            With Attenuated Refsum Disease
  JOURNAL   Invest Ophthalmol Vis Sci 65 (2), 38 (2024)
   PUBMED   38411969
  REMARK    GeneRIF: PHYH c.678+5G>T Leads to In-Frame Exon Skipping and Is
            Associated With Attenuated Refsum Disease.
REFERENCE   2  (bases 1 to 1541)
  AUTHORS   Zhengqi,Q., Zezhi,G., Lei,J., He,Q., Jinyao,P. and Ying,A.
  TITLE     Prognostic role of PHYH for overall survival (OS) in clear cell
            renal cell carcinoma (ccRCC)
  JOURNAL   Eur J Med Res 26 (1), 9 (2021)
   PUBMED   33468235
  REMARK    GeneRIF: Prognostic role of PHYH for overall survival (OS) in clear
            cell renal cell carcinoma (ccRCC).
            Publication Status: Online-Only
REFERENCE   3  (bases 1 to 1541)
  AUTHORS   Haenig,C., Atias,N., Taylor,A.K., Mazza,A., Schaefer,M.H., Russ,J.,
            Riechers,S.P., Jain,S., Coughlin,M., Fontaine,J.F., Freibaum,B.D.,
            Brusendorf,L., Zenkner,M., Porras,P., Stroedicke,M., Schnoegl,S.,
            Arnsburg,K., Boeddrich,A., Pigazzini,L., Heutink,P., Taylor,J.P.,
            Kirstein,J., Andrade-Navarro,M.A., Sharan,R. and Wanker,E.E.
  TITLE     Interactome Mapping Provides a Network of Neurodegenerative Disease
            Proteins and Uncovers Widespread Protein Aggregation in Affected
            Brains
  JOURNAL   Cell Rep 32 (7), 108050 (2020)
   PUBMED   32814053
REFERENCE   4  (bases 1 to 1541)
  AUTHORS   Luck,K., Kim,D.K., Lambourne,L., Spirohn,K., Begg,B.E., Bian,W.,
            Brignall,R., Cafarelli,T., Campos-Laborie,F.J., Charloteaux,B.,
            Choi,D., Cote,A.G., Daley,M., Deimling,S., Desbuleux,A., Dricot,A.,
            Gebbia,M., Hardy,M.F., Kishore,N., Knapp,J.J., Kovacs,I.A.,
            Lemmens,I., Mee,M.W., Mellor,J.C., Pollis,C., Pons,C.,
            Richardson,A.D., Schlabach,S., Teeking,B., Yadav,A., Babor,M.,
            Balcha,D., Basha,O., Bowman-Colin,C., Chin,S.F., Choi,S.G.,
            Colabella,C., Coppin,G., D'Amata,C., De Ridder,D., De Rouck,S.,
            Duran-Frigola,M., Ennajdaoui,H., Goebels,F., Goehring,L., Gopal,A.,
            Haddad,G., Hatchi,E., Helmy,M., Jacob,Y., Kassa,Y., Landini,S.,
            Li,R., van Lieshout,N., MacWilliams,A., Markey,D., Paulson,J.N.,
            Rangarajan,S., Rasla,J., Rayhan,A., Rolland,T., San-Miguel,A.,
            Shen,Y., Sheykhkarimli,D., Sheynkman,G.M., Simonovsky,E., Tasan,M.,
            Tejeda,A., Tropepe,V., Twizere,J.C., Wang,Y., Weatheritt,R.J.,
            Weile,J., Xia,Y., Yang,X., Yeger-Lotem,E., Zhong,Q., Aloy,P.,
            Bader,G.D., De Las Rivas,J., Gaudet,S., Hao,T., Rak,J.,
            Tavernier,J., Hill,D.E., Vidal,M., Roth,F.P. and Calderwood,M.A.
  TITLE     A reference map of the human binary protein interactome
  JOURNAL   Nature 580 (7803), 402-408 (2020)
   PUBMED   32296183
REFERENCE   5  (bases 1 to 1541)
  AUTHORS   Searls,T., Butler,D., Chien,W., Mukherji,M., Lloyd,M.D. and
            Schofield,C.J.
  TITLE     Studies on the specificity of unprocessed and mature forms of
            phytanoyl-CoA 2-hydroxylase and mutation of the iron binding
            ligands
  JOURNAL   J Lipid Res 46 (8), 1660-1667 (2005)
   PUBMED   15930519
  REMARK    GeneRIF: demonstrate that both unprocessed and processed forms are
            able to hydroxylate a range of CoA derivatives; site-directed
            mutagenesis was used to support proposals for the identity of the
            iron binding istes of PAHX
REFERENCE   6  (bases 1 to 1541)
  AUTHORS   Jansen,G.A., Wanders,R.J., Watkins,P.A. and Mihalik,S.J.
  TITLE     Phytanoyl-coenzyme A hydroxylase deficiency -- the enzyme defect in
            Refsum's disease
  JOURNAL   N Engl J Med 337 (2), 133-134 (1997)
   PUBMED   9221344
REFERENCE   7  (bases 1 to 1541)
  AUTHORS   Jansen,G.A., Mihalik,S.J., Watkins,P.A., Moser,H.W., Jakobs,C.,
            Denis,S. and Wanders,R.J.
  TITLE     Phytanoyl-CoA hydroxylase is present in human liver, located in
            peroxisomes, and deficient in Zellweger syndrome: direct,
            unequivocal evidence for the new, revised pathway of phytanic acid
            alpha-oxidation in humans
  JOURNAL   Biochem Biophys Res Commun 229 (1), 205-210 (1996)
   PUBMED   8954107
REFERENCE   8  (bases 1 to 1541)
  AUTHORS   Waterham,H.R., Wanders,R.J.A. and Leroy,B.P.
  TITLE     Adult Refsum Disease
  JOURNAL   (in) Adam MP, Feldman J, Mirzaa GM, Pagon RA, Wallace SE and
            Amemiya A (Eds.);
            GENEREVIEWS(R);
            (1993)
   PUBMED   20301527
REFERENCE   9  (bases 1 to 1541)
  AUTHORS   Perlman,S.
  TITLE     Hereditary Ataxia Overview
  JOURNAL   (in) Adam MP, Feldman J, Mirzaa GM, Pagon RA, Wallace SE and
            Amemiya A (Eds.);
            GENEREVIEWS(R);
            (1993)
   PUBMED   20301317
REFERENCE   10 (bases 1 to 1541)
  AUTHORS   Skjeldal,O.H., Stokke,O., Refsum,S., Norseth,J. and Petit,H.
  TITLE     Clinical and biochemical heterogeneity in conditions with phytanic
            acid accumulation
  JOURNAL   J Neurol Sci 77 (1), 87-96 (1987)
   PUBMED   2433405
COMMENT     REVIEWED REFSEQ: This record has been curated by NCBI staff. The
            reference sequence was derived from BC029512.1, AL138764.21 and
            BM351828.1.
            This sequence is a reference standard in the RefSeqGene project.
            
            On Nov 24, 2018 this sequence version replaced NM_006214.3.
            
            Summary: This gene is a member of the PhyH family and encodes a
            peroxisomal protein that is involved in the alpha-oxidation of
            3-methyl branched fatty acids. Specifically, this protein converts
            phytanoyl-CoA to 2-hydroxyphytanoyl-CoA. Mutations in this gene
            have been associated with Refsum disease (RD) and deficient protein
            activity has been associated with Zellweger syndrome and rhizomelic
            chondrodysplasia punctata. Alternate transcriptional splice
            variants, encoding different isoforms, have been characterized.
            [provided by RefSeq, Jul 2008].
            
            Transcript Variant: This variant (1) encodes isoform a.
            
            Publication Note:  This RefSeq record includes a subset of the
            publications that are available for this gene. Please see the Gene
            record to access additional publications.
            
            ##Evidence-Data-START##
            Transcript exon combination :: BC029512.1, SRR3476690.665677.1
                                           [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA2142586, SAMEA2146411
                                           [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            MANE Ensembl match     :: ENST00000263038.9/ ENSP00000263038.4
            RefSeq Select criteria :: based on conservation, expression
            ##RefSeq-Attributes-END##
            COMPLETENESS: full length.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-174               BC029512.1         27-200
            175-267             AL138764.21        124821-124913       c
            268-436             AL138764.21        123753-123921       c
            437-518             AL138764.21        121156-121237       c
            519-700             AL138764.21        117685-117866       c
            701-850             AL138764.21        113015-113164       c
            851-985             AL138764.21        110301-110435       c
            986-1537            AL138764.21        107128-107679       c
            1538-1541           BM351828.1         18-21               c
FEATURES             Location/Qualifiers
     source          1..1541
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="10"
                     /map="10p13"
     gene            1..1541
                     /gene="PHYH"
                     /gene_synonym="LN1; LNAP1; PAHX; PHYH1; RD"
                     /note="phytanoyl-CoA 2-hydroxylase"
                     /db_xref="GeneID:5264"
                     /db_xref="HGNC:HGNC:8940"
                     /db_xref="MIM:602026"
     exon            1..97
                     /gene="PHYH"
                     /gene_synonym="LN1; LNAP1; PAHX; PHYH1; RD"
                     /inference="alignment:Splign:2.1.0"
     CDS             23..1039
                     /gene="PHYH"
                     /gene_synonym="LN1; LNAP1; PAHX; PHYH1; RD"
                     /EC_number="1.14.11.18"
                     /note="isoform a precursor is encoded by transcript
                     variant 1; phytanoyl-CoA 2 oxoglutarate dioxygenase;
                     phytanic acid oxidase; phytanoyl-CoA alpha-hydroxylase;
                     phytanoil-CoA alpha hydroxylase; phytanoyl-CoA
                     dioxygenase, peroxisomal"
                     /codon_start=1
                     /product="phytanoyl-CoA dioxygenase, peroxisomal isoform a
                     precursor"
                     /protein_id="NP_006205.1"
                     /db_xref="CCDS:CCDS7097.1"
                     /db_xref="GeneID:5264"
                     /db_xref="HGNC:HGNC:8940"
                     /db_xref="MIM:602026"
                     /translation="MEQLRAAARLQIVLGHLGRPSAGAVVAHPTSGTISSASFHPQQF
                     QYTLDNNVLTLEQRKFYEENGFLVIKNLVPDADIQRFRNEFEKICRKEVKPLGLTVMR
                     DVTISKSEYAPSEKMITKVQDFQEDKELFRYCTLPEILKYVECFTGPNIMAMHTMLIN
                     KPPDSGKKTSRHPLHQDLHYFPFRPSDLIVCAWTAMEHISRNNGCLVVLPGTHKGSLK
                     PHDYPKWEGGVNKMFHGIQDYEENKARVHLVMEKGDTVFFHPLLIHGSGQNKTQGFRK
                     AISCHFASADCHYIDVKGTSQENIEKEVVGIAHKFFGAENSVNLKDIWMFRARLVKGE
                     RTNL"
     exon            98..156
                     /gene="PHYH"
                     /gene_synonym="LN1; LNAP1; PAHX; PHYH1; RD"
                     /inference="alignment:Splign:2.1.0"
     exon            157..267
                     /gene="PHYH"
                     /gene_synonym="LN1; LNAP1; PAHX; PHYH1; RD"
                     /inference="alignment:Splign:2.1.0"
     exon            268..436
                     /gene="PHYH"
                     /gene_synonym="LN1; LNAP1; PAHX; PHYH1; RD"
                     /inference="alignment:Splign:2.1.0"
     exon            437..518
                     /gene="PHYH"
                     /gene_synonym="LN1; LNAP1; PAHX; PHYH1; RD"
                     /inference="alignment:Splign:2.1.0"
     exon            519..700
                     /gene="PHYH"
                     /gene_synonym="LN1; LNAP1; PAHX; PHYH1; RD"
                     /inference="alignment:Splign:2.1.0"
     exon            701..850
                     /gene="PHYH"
                     /gene_synonym="LN1; LNAP1; PAHX; PHYH1; RD"
                     /inference="alignment:Splign:2.1.0"
     exon            851..985
                     /gene="PHYH"
                     /gene_synonym="LN1; LNAP1; PAHX; PHYH1; RD"
                     /inference="alignment:Splign:2.1.0"
     exon            986..1541
                     /gene="PHYH"
                     /gene_synonym="LN1; LNAP1; PAHX; PHYH1; RD"
                     /inference="alignment:Splign:2.1.0"
     regulatory      1517..1522
                     /regulatory_class="polyA_signal_sequence"
                     /gene="PHYH"
                     /gene_synonym="LN1; LNAP1; PAHX; PHYH1; RD"
                     /note="hexamer: AATAAA"
     polyA_site      1541
                     /gene="PHYH"
                     /gene_synonym="LN1; LNAP1; PAHX; PHYH1; RD"
                     /note="major polyA site"
ORIGIN      
        1 gggggttccc cgcgccgcag ccatggagca gcttcgcgcc gccgcccgtc tgcagattgt
       61 tctgggccac ctcggccgcc cctcggccgg ggctgtcgta gctcatccca cttcagggac
      121 tatttcctct gccagtttcc atcctcaaca attccagtat actctggata ataacgttct
      181 aaccctggaa cagagaaaat tttatgaaga aaatgggttt ctagtaatca aaaatcttgt
      241 acctgatgcc gatattcaac gctttcggaa tgagtttgaa aaaatctgca gaaaggaggt
      301 gaaaccatta ggattaacag taatgagaga tgtgaccatt tcgaaatccg aatatgctcc
      361 aagtgagaag atgatcacga aggtccagga tttccaggaa gataaggagc tcttcagata
      421 ctgcactctc cccgagattc tgaaatatgt ggagtgcttc actggaccta atattatggc
      481 catgcacaca atgttgataa acaaacctcc agattctggc aagaagacgt cccgtcaccc
      541 cctgcaccag gacctgcact atttcccctt caggcccagc gatctcatcg tttgcgcctg
      601 gacggcgatg gagcacatca gccggaacaa cggctgtctg gttgtgctcc caggcacaca
      661 caagggctcc ctgaagcccc acgattaccc caagtgggag gggggagtta acaaaatgtt
      721 ccacgggatc caggactacg aggaaaacaa ggcccgggtg cacctggtga tggagaaggg
      781 cgacactgtt ttcttccatc ctttgctcat ccacggatct ggtcagaata aaacccaggg
      841 attccggaag gcaatttcct gccatttcgc cagtgccgat tgccactaca ttgacgtgaa
      901 gggcaccagt caagaaaaca tcgagaagga agttgtagga atagcacata aattctttgg
      961 agctgaaaat agcgtgaact tgaaggatat ttggatgttt cgagctcgac ttgtgaaagg
     1021 agaaagaacc aatctttgaa atagccatct gctataactc tttcaacaga aaaccaaaac
     1081 caaacgaaat gtctaaggaa aatgttttct taatgagatg atgtaacctt ttctatcact
     1141 tgttaaaagc agaaaacatg tatcaggtac ttaattgcat agagttagtt ttgcagcaca
     1201 atggtgttgc tttaatggaa aaaaaaaaca gtaaaagtga aatattactg ttttaaggaa
     1261 aactaattta gggtggcagc caataaaggt ggttggtgtc taatttaagt gttaaatcaa
     1321 tttctttcat tcagttagct ctttacccaa gaagaagtga atgatttgga gcttagggta
     1381 tgttttgtat cccctttctg ataaacccat tccctaccaa ttttatgtca taagagattt
     1441 ttttccccca aatctagaac aatgtataat acattcacat ctagtcaagg gcataggaac
     1501 ggtgtcatgg agtccaaata aagtggatat tcctgctcgg a
//
