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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
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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

Expression

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  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

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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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

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