NUDT12 nudix hydrolase 12 [Homo sapiens (human)] - Gene

Summary

Official Symbol: NUDT12provided by HGNC
Official Full Name: nudix hydrolase 12provided by HGNC
Primary source: HGNC:HGNC:18826
See related: Ensembl:ENSG00000112874 MIM:609232; AllianceGenome:HGNC:18826
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Summary: Nucleotides are involved in numerous biochemical reactions and pathways within the cell as substrates, cofactors, and effectors. Nudix hydrolases, such as NUDT12, regulate the concentrations of individual nucleotides and of nucleotide ratios in response to changing circumstances (Abdelraheim et al., 2003 [PubMed 12790796]).[supplied by OMIM, Mar 2008]
Expression: Ubiquitous expression in kidney (RPKM 12.0), thyroid (RPKM 10.7) and 24 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 5q21.2

Exon count:: 7

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	5	NC_000005.10 (103548855..103562789, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	5	NC_060929.1 (104057169..104071102, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	5	NC_000005.9 (102884556..102898490, complement)

Chromosome 5 - NC_000005.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Decapping Enzyme NUDT12 Partners with BLMH for Cytoplasmic Surveillance of NAD-Capped RNAs.
Title: Decapping Enzyme NUDT12 Partners with BLMH for Cytoplasmic Surveillance of NAD-Capped RNAs.
The crystal structure of mouse Nudt12 in complex with the deNADding product AMP and three Mg(2+) ions at 1.6 A resolution provides insights into the molecular basis of the deNADding activity in the NAD pyrophosphate.
Title: Structural and mechanistic basis of mammalian Nudt12 RNA deNADding.
Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
NUDT12 may act to regulate the concentration of peroxisomal nicotinamide nucleotide cofactors required for oxidative metabolism in this organelle.
Title: Mammalian NADH diphosphatases of the Nudix family: cloning and characterization of the human peroxisomal NUDT12 protein.

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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

EBI GWAS Catalog

Description
A genome-wide association study in the genetic analysis of idiopathic thrombophilia project suggests sex-specific regulation of mitochondrial DNA levels. EBI GWAS Catalog EBI GWAS CatalogPubMed
A genome-wide association study of depressive symptoms. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association analyses suggest NELL1 influences adverse metabolic response to HCTZ in African Americans. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association study combining pathway analysis for typical sporadic amyotrophic lateral sclerosis in Chinese Han populations. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association study of smoking behaviours in patients with COPD. 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)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

D5S1802 (e-PCR)
- UniSTS:153698

SHGC-36365 (e-PCR)
- UniSTS:20875

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables NAD+ diphosphatase activity	IDA Inferred from Direct Assay more info	PubMed
enables NADH pyrophosphatase activity	IBA Inferred from Biological aspect of Ancestor more info
enables NADH pyrophosphatase activity	IDA Inferred from Direct Assay more info	PubMed
enables NADH pyrophosphatase activity	TAS Traceable Author Statement more info
enables NADPH pyrophosphatase activity	IEA Inferred from Electronic Annotation more info
enables RNA NAD-cap (NMN-forming) hydrolase activity	ISS Inferred from Sequence or Structural Similarity more info
enables magnesium ion binding	ISS Inferred from Sequence or Structural Similarity more info
enables phosphodiesterase decapping endonuclease activity	IMP Inferred from Mutant Phenotype more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables zinc ion binding	ISS Inferred from Sequence or Structural Similarity more info

Process	Evidence Code	Pubs
involved_in NAD biosynthesis via nicotinamide riboside salvage pathway	TAS Traceable Author Statement more info
involved_in NAD catabolic process	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within NAD catabolic process	IDA Inferred from Direct Assay more info	PubMed
involved_in NAD catabolic process	IDA Inferred from Direct Assay more info	PubMed
involved_in NAD-cap decapping	IDA Inferred from Direct Assay more info	PubMed
involved_in NADH metabolic process	IBA Inferred from Biological aspect of Ancestor more info
involved_in NADP catabolic process	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within NADP catabolic process	IDA Inferred from Direct Assay more info	PubMed
involved_in NADP catabolic process	IDA Inferred from Direct Assay more info	PubMed
involved_in circadian regulation of gene expression	ISS Inferred from Sequence or Structural Similarity more info
involved_in mRNA catabolic process	ISS Inferred from Sequence or Structural Similarity more info
involved_in mRNA methylguanosine-cap decapping	IDA Inferred from Direct Assay more info	PubMed

Component	Evidence Code	Pubs
located_in cytoplasm	IDA Inferred from Direct Assay more info	PubMed
located_in nucleus	IDA Inferred from Direct Assay more info
located_in peroxisomal matrix	TAS Traceable Author Statement more info
is_active_in peroxisome	IBA Inferred from Biological aspect of Ancestor more info
located_in peroxisome	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: NAD-capped RNA hydrolase NUDT12

Names: NADH pyrophosphatase NUDT12; deNADding enzyme NUDT12; nucleoside diphosphate linked moiety X-type motif 12; nucleoside diphosphate-linked moiety X motif 12; nudix (nucleoside diphosphate linked moiety X)-type motif 12; nudix motif 12; peroxisomal NADH pyrophosphatase NUDT12

NP_001287670.1

EC 3.6.1.22

NP_113626.1

EC 3.6.1.22

XP_005272152.1

EC 3.6.1.22

XP_005272154.1

EC 3.6.1.22

XP_054209565.1

EC 3.6.1.22

XP_054209566.1

EC 3.6.1.22

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)

NM_001300741.2 → NP_001287670.1 NAD-capped RNA hydrolase NUDT12 isoform 2

See identical proteins and their annotated locations for NP_001287670.1

Status: VALIDATED

Description

Transcript Variant: This variant (2) has an alternate splcie site in the 5' coding region but maintains the reading frame, compared to variant 1. The resulting isoform (2) lacks an internal segment, compared to isoform 1.

Source sequence(s)

AK304010, BC026748, DC417976

Consensus CDS

CCDS75284.1

UniProtKB/Swiss-Prot

Q9BQG2

UniProtKB/TrEMBL

B4E1W3, E7EM93

Related

ENSP00000424521.1, ENST00000507423.1

Conserved Domains (6) summary

COG2816
Location:108 → 437

NPY1; NADH pyrophosphatase NudC, Nudix superfamily [Nucleotide transport and metabolism]

cd00204
Location:14 → 80

ANK; ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other ...

cd03429
Location:305 → 438

NADH_pyrophosphatase; NADH pyrophosphatase, a member of the Nudix hydrolase superfamily, catalyzes the cleavage of NADH into reduced nicotinamide mononucleotide (NMNH) and AMP. Like other members of the Nudix family, it requires a divalent cation, such as Mg2+ or Mn2+, for ...

pfam09296
Location:130 → 259

NUDIX-like; NADH pyrophosphatase-like rudimentary NUDIX domain

pfam09297
Location:261 → 284

zf-NADH-PPase; NADH pyrophosphatase zinc ribbon domain

pfam12796
Location:16 → 80

Ank_2; Ankyrin repeats (3 copies)
NM_031438.4 → NP_113626.1 NAD-capped RNA hydrolase NUDT12 isoform 1

See identical proteins and their annotated locations for NP_113626.1

Status: VALIDATED

Description

Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).

Source sequence(s)

AK304010, BC026748, BC041099, DB029218

Consensus CDS

CCDS4096.1

UniProtKB/Swiss-Prot

B3KUW2, B4E1W3, Q8TAL7, Q9BQG2

Related

ENSP00000230792.2, ENST00000230792.7

Conserved Domains (3) summary

COG2816
Location:126 → 455

NPY1; NADH pyrophosphatase NudC, Nudix superfamily [Nucleotide transport and metabolism]

cd00204
Location:14 → 98

ANK; ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other ...

sd00045
Location:14 → 43

ANK; ANK repeat [structural motif]

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_000005.10 Reference GRCh38.p14 Primary Assembly

Range

103548855..103562789 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_005272097.4 → XP_005272154.1 NAD-capped RNA hydrolase NUDT12 isoform X2

See identical proteins and their annotated locations for XP_005272154.1

UniProtKB/TrEMBL

E7EM93

Conserved Domains (6) summary

COG2816
Location:108 → 437

NPY1; NADH pyrophosphatase NudC, Nudix superfamily [Nucleotide transport and metabolism]

cd00204
Location:14 → 80

ANK; ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other ...

cd03429
Location:305 → 438

NADH_pyrophosphatase; NADH pyrophosphatase, a member of the Nudix hydrolase superfamily, catalyzes the cleavage of NADH into reduced nicotinamide mononucleotide (NMNH) and AMP. Like other members of the Nudix family, it requires a divalent cation, such as Mg2+ or Mn2+, for ...

pfam09296
Location:130 → 259

NUDIX-like; NADH pyrophosphatase-like rudimentary NUDIX domain

pfam09297
Location:261 → 284

zf-NADH-PPase; NADH pyrophosphatase zinc ribbon domain

pfam12796
Location:16 → 80

Ank_2; Ankyrin repeats (3 copies)
XM_005272095.2 → XP_005272152.1 NAD-capped RNA hydrolase NUDT12 isoform X1

See identical proteins and their annotated locations for XP_005272152.1

UniProtKB/Swiss-Prot

B3KUW2, B4E1W3, Q8TAL7, Q9BQG2

Conserved Domains (3) summary

COG2816
Location:126 → 455

NPY1; NADH pyrophosphatase NudC, Nudix superfamily [Nucleotide transport and metabolism]

cd00204
Location:14 → 98

ANK; ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other ...

sd00045
Location:14 → 43

ANK; ANK repeat [structural motif]