NUDT13 nudix hydrolase 13 [Homo sapiens (human)] - Gene

Summary

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. Located in mitochondrion. [provided by Alliance of Genome Resources, Nov 2024]
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

Location:: 10q22.2

Exon count:: 11

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	10	NC_000010.11 (73110455..73131823)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	10	NC_060934.1 (73981847..74003215)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	10	NC_000010.10 (74870213..74891581)

Chromosome 10 - NC_000010.11 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?

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)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

STS-N33610 (e-PCR)
- UniSTS:73984

NUDT13_9439 (e-PCR)
- UniSTS:468561

RH79087 (e-PCR)
- UniSTS:26524

STS-W80642 (e-PCR)
- UniSTS:75765

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 NADPH pyrophosphatase activity	IEA Inferred from Electronic Annotation 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	HTP more info	PubMed
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

EC 3.6.1.22

NP_001269944.1

EC 3.6.1.22

NP_001269945.1

EC 3.6.1.22

NP_001269946.1

EC 3.6.1.22

NP_001269948.1

EC 3.6.1.22

NP_056985.3

EC 3.6.1.22

XP_024303694.1

EC 3.6.1.22

XP_047280940.1

EC 3.6.1.22

XP_047280941.1

EC 3.6.1.22

XP_054221418.1

EC 3.6.1.22

XP_054221419.1

EC 3.6.1.22

XP_054221420.1

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_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+ ...
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
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]
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 ...
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 ...
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

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_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000010.11 Reference GRCh38.p14 Primary Assembly

Range

73110455..73131823

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

Related

ENSP00000484185.1, ENST00000617744.4
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]
XM_047424985.1 → XP_047280941.1 NAD(P)H pyrophosphatase NUDT13, mitochondrial isoform X2

UniProtKB/TrEMBL

B4E059

Alternate T2T-CHM13v2.0

Genomic

NC_060934.1 Alternate T2T-CHM13v2.0

Range

73981847..74003215

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054365443.1 → XP_054221418.1 NAD(P)H pyrophosphatase NUDT13, mitochondrial isoform X1
XM_054365445.1 → XP_054221420.1 NAD(P)H pyrophosphatase NUDT13, mitochondrial isoform X3
XM_054365444.1 → XP_054221419.1 NAD(P)H pyrophosphatase NUDT13, mitochondrial isoform X2

UniProtKB/TrEMBL

B4E059