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

Summary

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

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_000001.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

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Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

IMPDH2 filaments protect from neurodegeneration in AMPD2 deficiency.
Title: IMPDH2 filaments protect from neurodegeneration in AMPD2 deficiency.
Delineating the phenotype and genetic basis of AMPD2-related pontocerebellar hypoplasia.
Title: Delineating the phenotype and genetic basis of AMPD2-related pontocerebellar hypoplasia.
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.
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.
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.
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.
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.
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.
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.
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 EBI GWAS CatalogPubMed

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

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

A006D12 (e-PCR)
- UniSTS:5946

MARC_6497-6498:996689707:1 (e-PCR)
- UniSTS:269662

D1S3693 (e-PCR)
- UniSTS:474271

MARC_5351-5352:996690313:1 (e-PCR)
- UniSTS:269491

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

EC 3.5.4.6

NP_001295099.1

EC 3.5.4.6

NP_001355738.1

EC 3.5.4.6

NP_004028.4

EC 3.5.4.6

NP_631895.1

EC 3.5.4.6

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

NG_034075.1 RefSeqGene

Range

5025..17239

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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.
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.
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.
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.
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

NC_000001.11 Reference GRCh38.p14 Primary Assembly

Range

109619837..109632055

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GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

NC_060925.1 Alternate T2T-CHM13v2.0

Range

109652557..109664776

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GenBank, FASTA, Sequence Viewer (Graphics)

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

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.