U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

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

Gene ID: 374659, updated on 25-Nov-2025
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, Jul 2025]
Expression
Ubiquitous expression in fat (RPKM 9.9), kidney (RPKM 7.9) and 25 other tissues See more
Orthologs
all
Try the new Gene page
Try the new Transcripts and proteins table
See HDDC3 in Genome Data Viewer
Location:
15q26.1
Exon count:
4
Annotation release Status Assembly Chr Location
RS_2025_08 current GRCh38.p14 (GCF_000001405.40) 15 NC_000015.10 (90929968..90932569, complement)
RS_2025_08 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (88689551..88694729, complement)
RS_2024_09 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

Go to nucleotide: Graphics FASTA GenBank

  • Project title: Tissue-specific circular RNA induction during human fetal development
  • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
  • BioProject: PRJNA270632
  • Publication: PMID 26076956
  • Analysis date: Mon Apr 2 22:54:59 2018

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. CFTR interactome mapping using the mammalian membrane two-hybrid high-throughput screening system. Lim SH, et al. Mol Syst Biol, 2022 Feb. PMID 35156780, Free PMC Article

See all (22) citations in PubMed

GeneRIFs: Gene References Into Functions

Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Products Interactant Other Gene Complex Source Pubs Description

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 guanosine-3',5'-bis(diphosphate) 3'-diphosphatase activity IEA
Inferred from Electronic Annotation
more info
  
enables hydrolase activity IEA
Inferred from Electronic Annotation
more info
  
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
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

NEW Try the new Transcript table

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_2025_08

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

    UniProtKB/TrEMBL
    H0YNP9
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.

Chemical Information
Molecular Biology Databases
Research Materials
Tools