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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
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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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