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    NUDT13 nudix hydrolase 13 [ Homo sapiens (human) ]

    Gene ID: 25961, updated on 7-Apr-2024

    Summary

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    Official Symbol
    NUDT13provided by HGNC
    Official Full Name
    nudix hydrolase 13provided by HGNC
    Primary source
    HGNC:HGNC:18827
    See related
    Ensembl:ENSG00000166321 MIM:609233; AllianceGenome:HGNC:18827
    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
    Predicted to enable NADH pyrophosphatase activity. Predicted to be involved in NADH metabolic process and NADP catabolic process. Predicted to be located in mitochondrion. [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Ubiquitous expression in testis (RPKM 2.0), skin (RPKM 1.9) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    Location:
    10q22.2
    Exon count:
    11
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 10 NC_000010.11 (73110455..73131823)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (73981847..74003215)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (74870213..74891581)

    Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:74778077-74778636 Neighboring gene ribosomal protein L17 pseudogene 50 Neighboring gene prolyl 4-hydroxylase subunit alpha 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3554 Neighboring gene H3K27ac hESC enhancer GRCh37_chr10:74856005-74856760 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3555 Neighboring gene ReSE screen-validated silencer GRCh37_chr10:74866945-74867185 Neighboring gene small nucleolar RNA, H/ACA box 11F Neighboring gene uncharacterized LOC124902452 Neighboring gene ecdysoneless cell cycle regulator Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:74927585-74928184 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:74928785-74929383 Neighboring gene family with sequence similarity 149 member B1 Neighboring gene uncharacterized LOC105378358

    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. Human knockouts and phenotypic analysis in a cohort with a high rate of consanguinity. Saleheen D, et al. Nature, 2017 Apr 12. PMID 28406212, Free PMC Article
    2. A systematic survey of loss-of-function variants in human protein-coding genes. MacArthur DG, et al. Science, 2012 Feb 17. PMID 22344438, Free PMC Article
    3. Identification of a large set of rare complete human knockouts. Sulem P, et al. Nat Genet, 2015 May. PMID 25807282
    4. Common homozygosity for predicted loss-of-function variants reveals both redundant and advantageous effects of dispensable human genes. Rausell A, et al. Proc Natl Acad Sci U S A, 2020 Jun 16. PMID 32487729, Free PMC Article
    5. The mutational constraint spectrum quantified from variation in 141,456 humans. Karczewski KJ, et al. Nature, 2020 May. PMID 32461654, Free PMC Article

    See all (19) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Observational study of gene-disease association. (HuGE Navigator)
      Title: Genetic variants in nuclear-encoded mitochondrial genes influence AIDS progression.
    Submit: New GeneRIF Correction

    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

    Copy number response

    Description
    Copy number response
    Triplosensitivity

    No evidence available (Last evaluated 2021-02-02)

    ClinGen Genome Curation Page
    Haploinsufficency

    Dosage sensitivity unlikely (Last evaluated 2021-02-02)

    ClinGen Genome Curation PagePubMed

    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

    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 NAD+ diphosphatase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables NADH pyrophosphatase activity ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables pyrophosphatase activity TAS
    Traceable Author Statement
    more info
    		  
    Process Evidence Code Pubs
    involved_in NADH metabolic process ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in NADP catabolic process ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in nucleobase-containing small molecule interconversion TAS
    Traceable Author Statement
    more info
    		  
    Component Evidence Code Pubs
    located_in mitochondrial matrix TAS
    Traceable Author Statement
    more info
    		  
    located_in mitochondrion ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  

    General protein information

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    Preferred Names
    NAD(P)H pyrophosphatase NUDT13, mitochondrial
    Names
    nucleoside diphosphate-linked moiety X motif 13
    nudix (nucleoside diphosphate linked moiety X)-type motif 13
    nudix motif 13
    NP_001269943.1
    NP_001269944.1
    NP_001269945.1
    NP_001269946.1
    NP_001269948.1
    NP_056985.3
    XP_024303694.1
    XP_047280940.1
    XP_047280941.1
    XP_054221418.1
    XP_054221419.1
    XP_054221420.1

    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.

    mRNA and Protein(s)

    1. NM_001283014.2 → NP_001269943.1  NAD(P)H pyrophosphatase NUDT13, mitochondrial isoform b

      See identical proteins and their annotated locations for NP_001269943.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks two alternate in-frame exons in the 3' coding region, compared to variant 1. This results in a shorter protein (isoform b), compared to isoform a.
      Source sequence(s)
      AL050114, BC046173, DB035851
      Consensus CDS
      CCDS60552.1
      UniProtKB/Swiss-Prot
      Q86X67
      Related
      ENSP00000335326.6, ENST00000349051.9
      Conserved Domains (3) summary
      pfam09296
      Location:49 → 162
      NUDIX-like; NADH pyrophosphatase-like rudimentary NUDIX domain
      pfam09297
      Location:166 → 195
      zf-NADH-PPase; NADH pyrophosphatase zinc ribbon domain
      cl00447
      Location:198 → 255
      Nudix_Hydrolase; Nudix hydrolase is a superfamily of enzymes found in all three kingdoms of life, and it catalyzes the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+ ...

    2. NM_001283015.2 → NP_001269944.1  NAD(P)H pyrophosphatase NUDT13, mitochondrial isoform c

      See identical proteins and their annotated locations for NP_001269944.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) lacks an exon in the coding region, which results in a frameshift and an early stop codon, compared to variant 1. The encoded isoform (c) is shorter and has a distinct C-terminus, compared to isoform a.
      Source sequence(s)
      AL050114, BC038833, DB035851
      Consensus CDS
      CCDS60551.1
      UniProtKB/TrEMBL
      A0A087X1G4
      Related
      ENSP00000362088.3, ENST00000372997.3
      Conserved Domains (2) summary
      pfam09296
      Location:49 → 162
      NUDIX-like; NADH pyrophosphatase-like rudimentary NUDIX domain
      pfam09297
      Location:166 → 195
      zf-NADH-PPase; NADH pyrophosphatase zinc ribbon domain

    3. NM_001283016.2 → NP_001269945.1  NAD(P)H pyrophosphatase NUDT13, mitochondrial isoform d

      See identical proteins and their annotated locations for NP_001269945.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) contains an alternate exon in the 5' UTR and initiates translation at a downstream start codon, compared to variant 1. The encoded isoform (d) is shorter than isoform a.
      Source sequence(s)
      AK300980, AL050114, DB035851
      Consensus CDS
      CCDS60553.1
      UniProtKB/Swiss-Prot
      Q86X67
      Related
      ENSP00000440760.1, ENST00000544879.5
      Conserved Domains (1) summary
      COG2816
      Location:9 → 217
      NPY1; NADH pyrophosphatase NudC, Nudix superfamily [Nucleotide transport and metabolism]

    4. NM_001283017.2 → NP_001269946.1  NAD(P)H pyrophosphatase NUDT13, mitochondrial isoform e

      See identical proteins and their annotated locations for NP_001269946.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (5) contains an alternate exon, lacks an alternate exon, and initiates translation at a downstream start codon, compared to variant 1. The encoded isoform (e) is shorter than isoform a. Variants 5 and 6 encode the same isoform (e).
      Source sequence(s)
      AK316538, AL050114, AL521667, DB035851
      Consensus CDS
      CCDS73148.1
      UniProtKB/TrEMBL
      B4E059
      Related
      ENSP00000438223.1, ENST00000537969.5
      Conserved Domains (1) summary
      cd03429
      Location:3 → 147
      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 ...

    5. NM_001283019.2 → NP_001269948.1  NAD(P)H pyrophosphatase NUDT13, mitochondrial isoform e

      See identical proteins and their annotated locations for NP_001269948.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (6) lacks an alternate exon and initiates translation at a downstream start codon, compared to variant 1. The encoded isoform (e) is shorter than isoform a. Variants 5 and 6 encode the same isoform (e).
      Source sequence(s)
      AK303235, AL050114, DB035851
      Consensus CDS
      CCDS73148.1
      UniProtKB/TrEMBL
      B4E059
      Conserved Domains (1) summary
      cd03429
      Location:3 → 147
      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 ...

    6. NM_015901.6 → NP_056985.3  NAD(P)H pyrophosphatase NUDT13, mitochondrial isoform a

      See identical proteins and their annotated locations for NP_056985.3

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) encodes the longest isoform (a).
      Source sequence(s)
      AL050114, AL521667, BC046173, DB035851
      Consensus CDS
      CCDS31220.1
      UniProtKB/Swiss-Prot
      B4DV90, O95650, Q5SQM4, Q5SQM5, Q5SQM6, Q86X67, Q9Y3X2
      Related
      ENSP00000349874.4, ENST00000357321.9
      Conserved Domains (4) summary
      COG2816
      Location:31 → 343
      NPY1; NADH pyrophosphatase NudC, Nudix superfamily [Nucleotide transport and metabolism]
      cd03429
      Location:200 → 344
      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:49 → 162
      NUDIX-like; NADH pyrophosphatase-like rudimentary NUDIX domain
      pfam09297
      Location:166 → 195
      zf-NADH-PPase; NADH pyrophosphatase zinc ribbon domain

    RNA

    1. NR_104264.2 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (7) uses an alternate splice site in an internal exon, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      BC031224, BC038833, DB035851
      Related
      ENST00000488223.5

    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_000010.11 Reference GRCh38.p14 Primary Assembly

      Range
      73110455..73131823
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047424984.1 → XP_047280940.1  NAD(P)H pyrophosphatase NUDT13, mitochondrial isoform X1

      Related
      ENSP00000484185.1, ENST00000617744.4

    2. XM_024447926.2 → XP_024303694.1  NAD(P)H pyrophosphatase NUDT13, mitochondrial isoform X3

      Conserved Domains (1) summary
      COG2816
      Location:9 → 217
      NPY1; NADH pyrophosphatase NudC, Nudix superfamily [Nucleotide transport and metabolism]

    3. XM_047424985.1 → XP_047280941.1  NAD(P)H pyrophosphatase NUDT13, mitochondrial isoform X2

      UniProtKB/TrEMBL
      B4E059

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060934.1 Alternate T2T-CHM13v2.0

      Range
      73981847..74003215
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054365443.1 → XP_054221418.1  NAD(P)H pyrophosphatase NUDT13, mitochondrial isoform X1

    2. XM_054365445.1 → XP_054221420.1  NAD(P)H pyrophosphatase NUDT13, mitochondrial isoform X3

    3. XM_054365444.1 → XP_054221419.1  NAD(P)H pyrophosphatase NUDT13, mitochondrial isoform X2

      UniProtKB/TrEMBL
      B4E059
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q86X67.3 GenPept UniProtKB/Swiss-Prot:Q86X67

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