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HDDC3 HD domain containing 3 [ Homo sapiens (human) ]

Gene ID: 374659, updated on 3-Apr-2024

Summary

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Official Symbol
HDDC3provided by HGNC
Official Full Name
HD domain containing 3provided by HGNC
Primary source
HGNC:HGNC:30522
See related
Ensembl:ENSG00000184508 AllianceGenome:HGNC:30522
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
Also known as
MESH1; MYNRL15; (ppGpp)ase
Summary
Predicted to enable guanosine-3',5'-bis(diphosphate) 3'-diphosphatase activity. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in fat (RPKM 9.9), kidney (RPKM 7.9) and 25 other tissues See more
Orthologs
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Genomic context

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Location:
15q26.1
Exon count:
4
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 15 NC_000015.10 (90929968..90932569, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (88689551..88694729, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 15 NC_000015.9 (91473198..91475799, complement)

Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6830 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10099 Neighboring gene FES proto-oncogene, tyrosine kinase Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10100 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6831 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6832 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10101 Neighboring gene mannosidase alpha class 2A member 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10102 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10103 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10104 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10105 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6833 Neighboring gene unc-45 myosin chaperone A Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:91496471-91496971 Neighboring gene H3K27ac hESC enhancer GRCh37_chr15:91497796-91498350 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6834 Neighboring gene RCCD1 and UNC45A antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6835 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6836 Neighboring gene RCC1 domain containing 1

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. MESH1 is a cytosolic NADPH phosphatase that regulates ferroptosis. Ding CC, et al. Nat Metab, 2020 Mar. PMID 32462112, Free PMC Article
  2. A metazoan ortholog of SpoT hydrolyzes ppGpp and functions in starvation responses. Sun D, et al. Nat Struct Mol Biol, 2010 Oct. PMID 20818390
  3. Analysis of the DNA sequence and duplication history of human chromosome 15. Zody MC, et al. Nature, 2006 Mar 30. PMID 16572171
  4. Spatiotemporal-resolved protein networks profiling with photoactivation dependent proximity labeling. Zhai Y, et al. Nat Commun, 2022 Aug 20. PMID 35987950, Free PMC Article
  5. Extensive disruption of protein interactions by genetic variants across the allele frequency spectrum in human populations. Fragoza R, et al. Nat Commun, 2019 Sep 12. PMID 31515488, Free PMC Article

See all (20) citations in PubMed

GeneRIFs: Gene References Into Functions

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

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

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • MGC45386

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables guanosine-3',5'-bis(diphosphate) 3'-diphosphatase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 

General protein information

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Preferred Names
guanosine-3',5'-bis(diphosphate) 3'-pyrophosphohydrolase MESH1
Names
HD domain-containing protein 3
metazoan SpoT homolog 1
myeloid leukemia noncoding regulatory locus on chromosome 15
penta-phosphate guanosine-3'-pyrophosphohydrolase
NP_001273380.1
NP_940929.1
XP_054233867.1
XP_054233868.1

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_001286451.2 → NP_001273380.1  guanosine-3',5'-bis(diphosphate) 3'-pyrophosphohydrolase MESH1 isoform 1

    See identical proteins and their annotated locations for NP_001273380.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the shortest transcript and encodes the longer isoform (1).
    Source sequence(s)
    AC068831
    Consensus CDS
    CCDS66866.1
    UniProtKB/Swiss-Prot
    Q8N4P3
    Related
    ENSP00000377814.4, ENST00000394272.8
    Conserved Domains (2) summary
    COG0317
    Location:4 → 137
    SpoT; (p)ppGpp synthase/hydrolase, HD superfamily [Signal transduction mechanisms, Transcription]
    pfam13328
    Location:11 → 138
    HD_4; HD domain

  2. NM_198527.4 → NP_940929.1  guanosine-3',5'-bis(diphosphate) 3'-pyrophosphohydrolase MESH1 isoform 2

    See identical proteins and their annotated locations for NP_940929.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) uses an alternate splice site in the 3' coding region, which results in a frameshift, compared to variant 1. The encoded isoform (2) has a distinct C-terminus and is shorter than isoform 1.
    Source sequence(s)
    AW138983, BC033794, BI833873, BQ187342
    Consensus CDS
    CCDS10366.1
    UniProtKB/TrEMBL
    H0YNP9
    Related
    ENSP00000330721.3, ENST00000330334.7
    Conserved Domains (1) summary
    COG0317
    Location:4 → 138
    SpoT; (p)ppGpp synthase/hydrolase, HD superfamily [Signal transduction mechanisms, Transcription]

RNA

  1. NR_104447.2 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) uses an alternate splice site in the 5' terminal 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)
    AC068831, AW138983, BQ777217, BU633661, CA450487

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_000015.10 Reference GRCh38.p14 Primary Assembly

    Range
    90929968..90932569 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060939.1 Alternate T2T-CHM13v2.0

    Range
    88689551..88694729 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054377892.1 → XP_054233867.1  guanosine-3',5'-bis(diphosphate) 3'-pyrophosphohydrolase MESH1 isoform X1

    UniProtKB/Swiss-Prot
    Q8N4P3

  2. XM_054377893.1 → XP_054233868.1  guanosine-3',5'-bis(diphosphate) 3'-pyrophosphohydrolase MESH1 isoform X2

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q8N4P3.3 GenPept UniProtKB/Swiss-Prot:Q8N4P3

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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