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

Gene ID: 271, updated on 14-Nov-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
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Genomic context

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See AMPD2 in Genome Data Viewer
Location:
1p13.3
Exon count:
20
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (109619837..109632055)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (109652557..109664776)
RS_2024_09 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 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. Cloning, sequence and characterization of the human AMPD2 gene: evidence for transcriptional regulation by two closely spaced promoters. Mahnke-Zizelman DK, et al. Biochim Biophys Acta, 1996 Aug 14. PMID 8764830
  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. N-terminal extensions of the human AMPD2 polypeptide influence ATP regulation of isoform L. Haas AL, et al. Biochem Biophys Res Commun, 2003 May 30. PMID 12745092

See all (65) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. IMPDH2 filaments protect from neurodegeneration in AMPD2 deficiency.
    Title: IMPDH2 filaments protect from neurodegeneration in AMPD2 deficiency.
  2. Delineating the phenotype and genetic basis of AMPD2-related pontocerebellar hypoplasia.
    Title: Delineating the phenotype and genetic basis of AMPD2-related pontocerebellar hypoplasia.
  3. 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.
  4. 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.
  5. 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.
  6. 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.
  7. 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.
  8. 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.
  9. 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.
  10. 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.
Submit: New GeneRIF Correction See all GeneRIFs (12)

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)

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 identical protein binding IPI
Inferred from Physical Interaction
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 ATP metabolic process IEA
Inferred from Electronic Annotation
more info
  
involved_in GTP metabolic process IEA
Inferred from Electronic Annotation
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 cholesterol homeostasis 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 
involved_in podocyte development IEA
Inferred from Electronic Annotation
more info
  
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_2024_08

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

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