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    AMD1 adenosylmethionine decarboxylase 1 [ Homo sapiens (human) ]

    Gene ID: 262, updated on 5-Mar-2024

    Summary

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    Official Symbol
    AMD1provided by HGNC
    Official Full Name
    adenosylmethionine decarboxylase 1provided by HGNC
    Primary source
    HGNC:HGNC:457
    See related
    Ensembl:ENSG00000123505 MIM:180980; AllianceGenome:HGNC:457
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    AMD; SAMDC; ADOMETDC
    Summary
    This gene encodes an important intermediate enzyme in polyamine biosynthesis. The polyamines spermine, spermidine, and putrescine are low-molecular-weight aliphatic amines essential for cellular proliferation and tumor promotion. Multiple alternatively spliced transcript variants have been identified. Pseudogenes of this gene are found on chromosomes 5, 6, 10, X and Y. [provided by RefSeq, Dec 2013]
    Expression
    Ubiquitous expression in prostate (RPKM 106.1), bone marrow (RPKM 38.6) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    Location:
    6q21
    Exon count:
    11
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (110814617..110895713)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (111993221..112074322)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (111135820..111216916)

    Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene cyclin dependent kinase 19 Neighboring gene uncharacterized LOC124901502 Neighboring gene RNA, U6 small nuclear 957, pseudogene Neighboring gene Sharpr-MPRA regulatory region 10405 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24936 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17467 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24937 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:111135767-111136319 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24938 Neighboring gene MPRA-validated peak6028 silencer Neighboring gene RNA, U6 small nuclear 1115, pseudogene Neighboring gene Sharpr-MPRA regulatory region 678 Neighboring gene small nucleolar RNA, H/ACA box 40C Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:111196410-111197125 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:111197126-111197840 Neighboring gene calponin 2 pseudogene 9 Neighboring gene RBIS pseudogene 4 Neighboring gene MPRA-validated peak6032 silencer Neighboring gene PDGFA associated protein 1 pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24939 Neighboring gene Sharpr-MPRA regulatory region 5639 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24940 Neighboring gene small nucleolar RNA U13 Neighboring gene general transcription factor IIIC subunit 6

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Bibliography

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    Related articles in PubMed

    1. Polyamine synthesis enzyme AMD1 is closely associated with tumorigenesis and prognosis of human gastric cancers. Xu L, et al. Carcinogenesis, 2020 Apr 22. PMID 31140554
    2. Polyamine Regulator AMD1 Promotes Cell Migration in Epidermal Wound Healing. Lim HK, et al. J Invest Dermatol, 2018 Dec. PMID 29906410
    3. AMD1 mRNA employs ribosome stalling as a mechanism for molecular memory formation. Yordanova MM, et al. Nature, 2018 Jan 18. PMID 29310120
    4. Chaotic neovascularization induced by aggressive fibrosarcoma cells overexpressing S-adenosylmethionine decarboxylase. Paasinen-Sohns A, et al. Int J Biochem Cell Biol, 2011 Mar. PMID 21134486
    5. Role of the sulfonium center in determining the ligand specificity of human s-adenosylmethionine decarboxylase. Bale S, et al. Biochemistry, 2009 Jul 14. PMID 19527050, Free PMC Article

    See all (62) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. AMD1 is required for the maintenance of leukemic stem cells and promotes chronic myeloid leukemic growth.
      Title: AMD1 is required for the maintenance of leukemic stem cells and promotes chronic myeloid leukemic growth.
    2. Polyamine synthesis enzyme AMD1 is closely associated with tumorigenesis and prognosis of human gastric cancers.
      Title: Polyamine synthesis enzyme AMD1 is closely associated with tumorigenesis and prognosis of human gastric cancers.
    3. Three SNPs (RUNX3 rs7553295 G > T, AMD1 rs1279590 G > A and MSRA rs73534533 C > A) were replicated in the validation dataset, and their meta-analysis showed an adjusted hazards ratio [HR] of 0.82 [95% confidence interval (CI) =0.75-0.89] and pmeta = 2.86 x 10(-6) , 0.81 (0.73-0.91) and pmeta = 4.63 x 10(-4) , and 0.77 (0.68-0.89) and pmeta = 2.07 x 10(-4) , respectively).
      Title: Genetic variants in RUNX3, AMD1 and MSRA in the methionine metabolic pathway and survival in nonsmall cell lung cancer patients.
    4. this study shows that AMD1 promotes cell migration in epidermal wound healimg
      Title: Polyamine Regulator AMD1 Promotes Cell Migration in Epidermal Wound Healing.
    5. AMD1 mRNA employs ribosome stalling as a mechanism for molecular memory formation
      Title: AMD1 mRNA employs ribosome stalling as a mechanism for molecular memory formation.
    6. AMD1 is upregulated in human prostate cancer with activated mTORC1
      Title: mTORC1-dependent AMD1 regulation sustains polyamine metabolism in prostate cancer.
    7. AMD1 gene variants previously found to associate among Indian children did not associate with risk of obesity or obesity-related quantitative measures among Caucasian children and juvenile men from Denmark.
      Title: Common variants in LEPR, IL6, AMD1, and NAMPT do not associate with risk of juvenile and childhood obesity in Danes: a case-control study.
    8. (AMD1)-mediated mRNA processing and cell adhesion activated & inhibited transition mechanisms
      Title: Adenosylmethionine decarboxylase 1 (AMD1)-mediated mRNA processing and cell adhesion activated & inhibited transition mechanisms by different comparisons between chimpanzee and human left hemisphere.
    9. Gene expression studies have identified altered expression of AMD1 in suicide completers with a history of mood disorders.
      Title: Effects of promoter methylation on increased expression of polyamine biosynthetic genes in suicide.
    10. This study demomistrated that H3K4me3 modification plays an important role in up regulation of AMD1 in prefrontal cortex.
      Title: Effects of histone modifications on increased expression of polyamine biosynthetic genes in suicide.
    Submit: New GeneRIF Correction See all GeneRIFs (22)

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    HIV-1 interactions

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    Protein interactions

    Protein Gene Interaction Pubs
    Rev rev Inhibition of S-adenosylmethionine decarboxylase, a key enzyme in polyamine biosynthesis, compromises hypusine modification and activation of eukaryotic initiation factor 5A (eIF-5A), a cellular cofactor of HIV-1 Rev, and inhibits Rev function PubMed

    Go to the HIV-1, Human Interaction Database

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ26964, DKFZp313L1234

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables adenosylmethionine decarboxylase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables adenosylmethionine decarboxylase activity TAS
    Traceable Author Statement
    more info
    		 PubMed 
    enables identical protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables putrescine binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Process Evidence Code Pubs
    involved_in polyamine metabolic process TAS
    Traceable Author Statement
    more info
    		  
    involved_in spermidine biosynthetic process IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in spermine biosynthetic process IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    is_active_in cytosol IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cytosol TAS
    Traceable Author Statement
    more info
    		  

    General protein information

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    Preferred Names
    S-adenosylmethionine decarboxylase proenzyme
    Names
    S-adenosylmethionine decarboxylase 1
    NP_001274143.1
    NP_001274144.1
    NP_001274145.1
    NP_001380335.1
    NP_001380336.1
    NP_001380337.1
    NP_001625.2

    NCBI Reference Sequences (RefSeq)

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    NEW Try the new Transcript table

    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    mRNA and Protein(s)

    1. NM_001287214.1 → NP_001274143.1  S-adenosylmethionine decarboxylase proenzyme isoform 3

      See identical proteins and their annotated locations for NP_001274143.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) lacks an in-frame exon in the coding region, compared to variant 1. The resulting isoform (3) lacks an internal segment, compared to isoform 1.
      Source sequence(s)
      AA808049, AK130474, AK300330, AK302761
      UniProtKB/TrEMBL
      A0A088AWN0, Q6N0B2
      Conserved Domains (1) summary
      pfam01536
      Location:4 → 296
      SAM_decarbox; Adenosylmethionine decarboxylase

    2. NM_001287215.2 → NP_001274144.1  S-adenosylmethionine decarboxylase proenzyme isoform 4 precursor

      See identical proteins and their annotated locations for NP_001274144.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) has an alternate 5' exon, which results in translation initiation at a downstream AUG start codon, compared to variant 1. The resulting isoform (4) has a shorter N-terminus, compared to isoform 1. Variants 4 and 7 both encode the same isoform (4).
      Source sequence(s)
      AA808049, AK130474, AK304351, Z84480
      Consensus CDS
      CCDS75505.1
      UniProtKB/TrEMBL
      A6NNH3, B4DTR6, Q5VXN5
      Related
      ENSP00000357870.1, ENST00000368876.2
      Conserved Domains (1) summary
      pfam01536
      Location:1 → 256
      SAM_decarbox; Adenosylmethionine decarboxylase

    3. NM_001287216.1 → NP_001274145.1  S-adenosylmethionine decarboxylase proenzyme isoform 5

      See identical proteins and their annotated locations for NP_001274145.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (5) lacks consecutive four exons in the coding region, but maintains the reading frame, compared to variant 1. The resulting isoform (5) lacks an internal segment, compared to isoform 1.
      Source sequence(s)
      AA808049, AK130474, AK302761
      Consensus CDS
      CCDS75504.1
      UniProtKB/TrEMBL
      B4DZ60
      Related
      ENSP00000502112.1, ENST00000675380.1
      Conserved Domains (1) summary
      cl03253
      Location:4 → 205
      SAM_decarbox; Adenosylmethionine decarboxylase

    4. NM_001393406.1 → NP_001380335.1  S-adenosylmethionine decarboxylase proenzyme isoform 4 precursor

      Status: REVIEWED

      Source sequence(s)
      AL357515, AL365206
      Consensus CDS
      CCDS75505.1
      UniProtKB/TrEMBL
      A6NNH3, B4DTR6, Q5VXN5
      Related
      ENSP00000357871.6, ENST00000368877.9
      Conserved Domains (1) summary
      pfam01536
      Location:1 → 256
      SAM_decarbox; Adenosylmethionine decarboxylase

    5. NM_001393407.1 → NP_001380336.1  S-adenosylmethionine decarboxylase proenzyme isoform 6

      Status: REVIEWED

      Description
      Transcript Variant: This variant (8), as well as variant 9, encodes isoform 6.
      Source sequence(s)
      AL357515, AL365206
      Conserved Domains (1) summary
      pfam01536
      Location:1 → 208
      SAM_decarbox; Adenosylmethionine decarboxylase

    6. NM_001393408.1 → NP_001380337.1  S-adenosylmethionine decarboxylase proenzyme isoform 6

      Status: REVIEWED

      Description
      Transcript Variant: This variant (9), as well as variant 8, encodes isoform 6.
      Source sequence(s)
      AL357515, AL365206
      Conserved Domains (1) summary
      pfam01536
      Location:1 → 208
      SAM_decarbox; Adenosylmethionine decarboxylase

    7. NM_001634.6 → NP_001625.2  S-adenosylmethionine decarboxylase proenzyme isoform 1

      See identical proteins and their annotated locations for NP_001625.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
      Source sequence(s)
      AL357515, AL365206
      Consensus CDS
      CCDS5086.1
      UniProtKB/Swiss-Prot
      E1P5F7, P17707, Q5VXN4, Q5VXN6, Q9BWK4
      UniProtKB/TrEMBL
      Q6N0B2
      Related
      ENSP00000357880.3, ENST00000368885.8
      Conserved Domains (1) summary
      pfam01536
      Location:4 → 325
      SAM_decarbox; Adenosylmethionine decarboxylase

    RNA

    1. NR_109768.2 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (6) lacks three consecutive internal exons, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AA808049, AK302761, AL832698
      Related
      ENST00000451850.6

    2. NR_171681.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AL357515, AL365206

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000006.12 Reference GRCh38.p14 Primary Assembly

      Range
      110814617..110895713
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060930.1 Alternate T2T-CHM13v2.0

      Range
      111993221..112074322
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_001033059.1: Suppressed sequence

      Description
      NM_001033059.1: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    P17707.2 GenPept UniProtKB/Swiss-Prot:P17707

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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