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    AMPD2 adenosine monophosphate deaminase 2 [ Homo sapiens (human) ]

    Gene ID: 271, updated on 22-Apr-2024

    Summary

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    Official Symbol
    AMPD2provided by HGNC
    Official Full Name
    adenosine monophosphate deaminase 2provided by HGNC
    Primary source
    HGNC:HGNC:469
    See related
    Ensembl:ENSG00000116337 MIM:102771; AllianceGenome:HGNC:469
    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
    AMPD; PCH9; SPG63
    Summary
    The protein encoded by this gene is important in purine metabolism by converting AMP to IMP. The encoded protein, which acts as a homotetramer, is one of three AMP deaminases found in mammals. Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Apr 2012]
    Expression
    Ubiquitous expression in bone marrow (RPKM 34.7), adrenal (RPKM 15.5) and 24 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    Location:
    1p13.3
    Exon count:
    20
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (109619837..109632055)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (109652557..109664776)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (110162459..110174677)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene G protein subunit alpha i3 Neighboring gene MPRA-validated peak357 silencer Neighboring gene microRNA 197 Neighboring gene G protein subunit alpha transducin 2 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:110161626-110162156 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:110162157-110162685 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:110163216-110163744 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1448 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:110164805-110165334 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:110166705-110167518 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr1:110170748-110171947 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:110171947-110172506 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:110173069-110173628 Neighboring gene Sharpr-MPRA regulatory region 1493 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:110186678-110187551 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1449 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:110199362-110199947 Neighboring gene ribosomal protein L7 pseudogene 8 Neighboring gene glutathione S-transferase mu 4

    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. Delineating the phenotype and genetic basis of AMPD2-related pontocerebellar hypoplasia. Gilboa T, et al. Neurogenetics, 2023 Jan. PMID 36445597
    2. Functional genomics identifies AMPD2 as a new prognostic marker for undifferentiated pleomorphic sarcoma. Orth MF, et al. Int J Cancer, 2019 Feb 15. PMID 30267407
    3. Clinical and genetic spectrum of AMPD2-related pontocerebellar hypoplasia type 9. Kortüm F, et al. Eur J Hum Genet, 2018 May. PMID 29463858, Free PMC Article
    4. A novel AMPD2 mutation outside the AMP deaminase domain causes pontocerebellar hypoplasia type 9. Marsh AP, et al. Am J Med Genet A, 2017 Mar. PMID 28168832
    5. Effects of tofacitinib on nucleic acid metabolism in human articular chondrocytes. Koizumi H, et al. Mod Rheumatol, 2015 Jul. PMID 25496463

    See all (59) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Delineating the phenotype and genetic basis of AMPD2-related pontocerebellar hypoplasia.
      Title: Delineating the phenotype and genetic basis of AMPD2-related pontocerebellar hypoplasia.
    2. Homozygous variants in AMPD2 and COL11A1 lead to a complex phenotype of pontocerebellar hypoplasia type 9 and Stickler syndrome type 2.
      Title: Homozygous variants in AMPD2 and COL11A1 lead to a complex phenotype of pontocerebellar hypoplasia type 9 and Stickler syndrome type 2.
    3. These data demonstrate a novel mechanism in Systemic lupus erythematosus development that involves the targeting of AMPD2 expression by NovelmiRNA-25.
      Title: NovelmiRNA-25 inhibits AMPD2 in peripheral blood mononuclear cells of patients with systemic lupus erythematosus and represents a promising novel biomarker.
    4. Data suggest that adenosine monophosphate deaminase 2 (AMPD2) may serve as a biomarker for outcome prediction in undifferentiated pleomorphic sarcoma (UPS).
      Title: Functional genomics identifies AMPD2 as a new prognostic marker for undifferentiated pleomorphic sarcoma.
    5. The existence of various AMPD2 isoforms with different functions possibly explains the variability in phenotypes associated with AMPD2 variants: variants leaving some of the isoforms intact may cause spastic paraplegia type 63 , while those affecting all isoforms may result in the severe and early-onset Pontocerebellar hypoplasia type 9.
      Title: Clinical and genetic spectrum of AMPD2-related pontocerebellar hypoplasia type 9.
    6. Here we report the clinical and genetic analysis of an individual with PCH9 secondary to a novel missense variant with strong evidence of pathogenicity, located outside the catalytic domain of AMPD2
      Title: A novel AMPD2 mutation outside the AMP deaminase domain causes pontocerebellar hypoplasia type 9.
    7. tofacitinib increases the cellular levels of adenosine, which is known to have anti-inflammatory activity, through the downregulation of AMPD2. This would be a novel functional aspect of tofacitinib.
      Title: Effects of tofacitinib on nucleic acid metabolism in human articular chondrocytes.
    8. In human HepG2 cells, AMPD2 activation counterregulates AMPK and increases intracellular glucose production, in association with up-regulation of PEPCK and G6Pc.
      Title: Uric acid-dependent inhibition of AMP kinase induces hepatic glucose production in diabetes and starvation: evolutionary implications of the uricase loss in hominids.
    9. Study concluded that AMPD2 as necessary for guanine nucleotide biosynthesis and protein translation and provide evidence that AMP deaminase activity is critical during neurogenesis. Patients with mutations in AMPD2 have characteristic brain imaging features of pontocerebellar hypoplasia due to loss of brainstem and cerebellar parenchyma.
      Title: AMPD2 regulates GTP synthesis and is mutated in a potentially treatable neurodegenerative brainstem disorder.
    10. Observational study of gene-disease association, gene-gene interaction, gene-environment interaction, and genetic testing. (HuGE Navigator)
      Title: Integrative predictive model of coronary artery calcification in atherosclerosis.
    Submit: New GeneRIF Correction See all GeneRIFs (11)

    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

    Associated conditions

    Description Tests
    Hereditary spastic paraplegia 63
    MedGen: C3810295 OMIM: 615686 GeneReviews: Not available
    		Compare labs
    Pontocerebellar hypoplasia type 9
    MedGen: C4014354 OMIM: 615809 GeneReviews: Not available
    		Compare labs

    EBI GWAS Catalog

    Description
    Genome-wide association study of recurrent early-onset major depressive disorder.
    EBI GWAS Catalog

    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
    retropepsin gag-pol Positional proteomics analysis identifies the cleavage of human adenosine monophosphate deaminase 2 (AMPD2) at amino acid residues 147-148 by the HIV-1 protease 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

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables AMP deaminase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables AMP deaminase activity IGI
    Inferred from Genetic Interaction
    more info
    		 PubMed 
    enables AMP deaminase activity NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in AMP metabolic process IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in IMP biosynthetic process IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within IMP biosynthetic process IGI
    Inferred from Genetic Interaction
    more info
    		 PubMed 
    involved_in IMP salvage IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in cyclic purine nucleotide metabolic process IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within energy homeostasis IGI
    Inferred from Genetic Interaction
    more info
    		 PubMed 
    Component Evidence Code Pubs
    is_active_in cytosol IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
    		  
    located_in cytosol TAS
    Traceable Author Statement
    more info
    		  

    General protein information

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    Preferred Names
    AMP deaminase 2
    Names
    adenosine monophosphate deaminase 2 (isoform L)
    NP_001244290.1
    NP_001295099.1
    NP_001355738.1
    NP_004028.4
    NP_631895.1

    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.

    Genomic

    1. NG_034075.1 RefSeqGene

      Range
      5025..17239
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001257361.2 → NP_001244290.1  AMP deaminase 2 isoform 4

      See identical proteins and their annotated locations for NP_001244290.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (5) lacks two alternate 5' exons and contains another compared to variant 4. The resulting isoform (4) is shorter at the N-terminus compared to isoform 1.
      Source sequence(s)
      AK296394, BC030217, DC410161, U16270
      Consensus CDS
      CCDS58016.1
      UniProtKB/TrEMBL
      H0YF16
      Related
      ENSP00000437164.1, ENST00000528454.5
      Conserved Domains (1) summary
      cd01319
      Location:237 → 733
      AMPD; AMP deaminase (AMPD) catalyzes the hydrolytic deamination of adensosine monophosphate (AMP) at position 6 of the adenine nucleotide ring. AMPD is a diverse and highly regulated eukaryotic key enzyme of the adenylate catabolic pathway.

    2. NM_001308170.1 → NP_001295099.1  AMP deaminase 2 isoform 5

      See identical proteins and their annotated locations for NP_001295099.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (6) differs in the 5' UTR and lacks an exon in the 5' coding region compared to variant 4. This variant represents translation initiation at an alternate start codon compared to variant 4; the 5'-most initiation codon, as used in variant 4, is associated with a truncated ORF that would render the transcript a candidate for nonsense-mediated decay (NMD). Leaky scanning may allow translation initiation at an alternate start codon to encode an isoform (5) that is shorter and has a distinct N-terminus, compared to isoform 1.
      Source sequence(s)
      AK302939, BC007711, BC030217, U16268
      UniProtKB/TrEMBL
      H0YF16
      Related
      ENSP00000437025.2, ENST00000476688.3
      Conserved Domains (1) summary
      cd01319
      Location:280 → 776
      AMPD; AMP deaminase (AMPD) catalyzes the hydrolytic deamination of adensosine monophosphate (AMP) at position 6 of the adenine nucleotide ring. AMPD is a diverse and highly regulated eukaryotic key enzyme of the adenylate catabolic pathway.

    3. NM_001368809.2 → NP_001355738.1  AMP deaminase 2 isoform 1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) represents the longest transcript and encodes the longest isoform (1). Variants 1 and 4 both encode the same isoform (1).
      Source sequence(s)
      AL355310
      Consensus CDS
      CCDS805.2
      UniProtKB/Swiss-Prot
      A0A5F9UK94, B4DK50, B4DZI5, E9PNG0, Q01433, Q14856, Q14857, Q16686, Q16687, Q16688, Q16729, Q5T693, Q5T695, Q96IA1, Q9UDX8, Q9UDX9, Q9UMU4
      UniProtKB/TrEMBL
      H0Y360
      Related
      ENSP00000436541.2, ENST00000528667.7
      Conserved Domains (1) summary
      cd01319
      Location:301 → 797
      AMPD; AMP deaminase (AMPD) catalyzes the hydrolytic deamination of adensosine monophosphate (AMP) at position 6 of the adenine nucleotide ring. AMPD is a diverse and highly regulated eukaryotic key enzyme of the adenylate catabolic pathway.

    4. NM_004037.9 → NP_004028.4  AMP deaminase 2 isoform 1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) differs in the 5' UTR compared to variant 4. Variants 1 and 4 both encode the longest isoform (1).
      Source sequence(s)
      AL355310
      Consensus CDS
      CCDS805.2
      UniProtKB/Swiss-Prot
      A0A5F9UK94, B4DK50, B4DZI5, E9PNG0, Q01433, Q14856, Q14857, Q16686, Q16687, Q16688, Q16729, Q5T693, Q5T695, Q96IA1, Q9UDX8, Q9UDX9, Q9UMU4
      UniProtKB/TrEMBL
      H0Y360
      Related
      ENSP00000256578.4, ENST00000256578.8
      Conserved Domains (1) summary
      cd01319
      Location:301 → 797
      AMPD; AMP deaminase (AMPD) catalyzes the hydrolytic deamination of adensosine monophosphate (AMP) at position 6 of the adenine nucleotide ring. AMPD is a diverse and highly regulated eukaryotic key enzyme of the adenylate catabolic pathway.

    5. NM_139156.4 → NP_631895.1  AMP deaminase 2 isoform 2

      See identical proteins and their annotated locations for NP_631895.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks the exon containing the translational start site compared to variant 4. The resulting isoform (2) has a shorter and distinct N-terminus compared to isoform 1.
      Source sequence(s)
      BC007711, DA558264
      Consensus CDS
      CCDS804.1
      UniProtKB/TrEMBL
      H0Y360
      Related
      ENSP00000345498.4, ENST00000342115.8
      Conserved Domains (1) summary
      cd01319
      Location:274 → 770
      AMPD; AMP deaminase (AMPD) catalyzes the hydrolytic deamination of adensosine monophosphate (AMP) at position 6 of the adenine nucleotide ring. AMPD is a diverse and highly regulated eukaryotic key enzyme of the adenylate catabolic pathway.

    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_000001.11 Reference GRCh38.p14 Primary Assembly

      Range
      109619837..109632055
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      109652557..109664776
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_203404.1: Suppressed sequence

      Description
      NM_203404.1: This RefSeq was removed because currently there is insufficient support for the transcript and the protein.
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q01433.3 GenPept UniProtKB/Swiss-Prot:Q01433

    Gene LinkOut

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

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