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    HIGD1A HIG1 hypoxia inducible domain family member 1A [ Homo sapiens (human) ]

    Gene ID: 25994, updated on 27-Nov-2024

    Summary

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    Official Symbol
    HIGD1Aprovided by HGNC
    Official Full Name
    HIG1 hypoxia inducible domain family member 1Aprovided by HGNC
    Primary source
    HGNC:HGNC:29527
    See related
    Ensembl:ENSG00000181061 MIM:618623; AllianceGenome:HGNC:29527
    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
    HIG1; RCF1a
    Summary
    Acts upstream of or within negative regulation of apoptotic process. Located in mitochondrion and nucleoplasm. Part of protein-containing complex. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Ubiquitous expression in colon (RPKM 73.6), heart (RPKM 47.7) and 24 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See HIGD1A in Genome Data Viewer
    Location:
    3p22.1
    Exon count:
    4
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (42782908..42804490, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (42800951..42820082, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (42824400..42845982, complement)

    Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene coiled-coil domain containing 13 Neighboring gene Sharpr-MPRA regulatory region 2509 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:42774613-42775298 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:42775299-42775982 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr3:42777355-42778040 Neighboring gene CCDC13 antisense RNA 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:42788170-42788670 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:42788671-42789171 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14250 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19750 Neighboring gene CCDC13 antisense RNA 2 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14251 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr3:42847019-42847816 Neighboring gene MIX23 pseudogene 4 Neighboring gene Sharpr-MPRA regulatory region 10622 Neighboring gene atypical chemokine receptor 2 Neighboring gene uncharacterized LOC124909373 Neighboring gene Sharpr-MPRA regulatory region 4247 Neighboring gene Sharpr-MPRA regulatory region 10602 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:42916634-42916810 Neighboring gene cytochrome P450 family 8 subfamily B member 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. The function role of HIGD1A in nonalcoholic steatohepatitis from chronic hepatitis B. Li MR, et al. Scand J Gastroenterol, 2024 Apr. PMID 38053282
    2. HIG1, a novel regulator of mitochondrial γ-secretase, maintains normal mitochondrial function. Hayashi H, et al. FASEB J, 2012 Jun. PMID 22355194
    3. HIGD1A inactivated by DNA hypermethylation promotes invasion of kidney renal clear cell carcinoma. Li L, et al. Pathol Res Pract, 2023 May. PMID 37086631
    4. HIG1 domain family member 1A is a crucial regulator of disorders associated with hypoxia. Jia YZ, et al. Mitochondrion, 2023 Mar. PMID 36804467
    5. Higd1a is a positive regulator of cytochrome c oxidase. Hayashi T, et al. Proc Natl Acad Sci U S A, 2015 Feb 3. PMID 25605899, Free PMC Article

    See all (76) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. The function role of HIGD1A in nonalcoholic steatohepatitis from chronic hepatitis B.
      Title: The function role of HIGD1A in nonalcoholic steatohepatitis from chronic hepatitis B.
    2. Mitochondrial HIGD1A inhibits hepatitis B virus transcription and replication through the cellular PNKD-NF-kappaB-NR2F1 nexus.
      Title: Mitochondrial HIGD1A inhibits hepatitis B virus transcription and replication through the cellular PNKD-NF-κB-NR2F1 nexus.
    3. HIGD1A inactivated by DNA hypermethylation promotes invasion of kidney renal clear cell carcinoma.
      Title: HIGD1A inactivated by DNA hypermethylation promotes invasion of kidney renal clear cell carcinoma.
    4. HIG1 domain family member 1A is a crucial regulator of disorders associated with hypoxia.
      Title: HIG1 domain family member 1A is a crucial regulator of disorders associated with hypoxia.
    5. HIG1 domain family member 1A disrupts proliferation, migration, and invasion of colon adenocarcinoma cells.
      Title: HIG1 domain family member 1A disrupts proliferation, migration, and invasion of colon adenocarcinoma cells.
    6. Distinct Roles of Mitochondrial HIGD1A and HIGD2A in Respiratory Complex and Supercomplex Biogenesis.
      Title: Distinct Roles of Mitochondrial HIGD1A and HIGD2A in Respiratory Complex and Supercomplex Biogenesis.
    7. Higd1a, or its mimic, provides therapeutic options for the treatment of mitochondrial diseases.
      Title: Higd1a improves respiratory function in the models of mitochondrial disorder.
    8. High Higd-1a expression is associated with proliferation of pancreatic cancer cells through a pERK/p27/pRB pathway.
      Title: Higd-1a regulates the proliferation of pancreatic cancer cells through a pERK/p27(KIP1)/pRB pathway.
    9. Higd1a plays positive roles in protecting cells from oxidative stress, and reactive oxygen species could induce Higd1a expression by upregulating PGC-1a and HIF-1a expressions.
      Title: Higd1a Protects Cells from Lipotoxicity under High-Fat Exposure.
    10. Nuclear localization of the mitochondrial factor HIGD1A during metabolic stress.
      Title: Nuclear localization of the mitochondrial factor HIGD1A during metabolic stress.
    Submit: New GeneRIF Correction See all GeneRIFs (13)

    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

    EBI GWAS Catalog

    Description
    Clozapine-induced agranulocytosis is associated with rare HLA-DQB1 and HLA-B alleles.
    EBI GWAS Catalog
    Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population.
    EBI GWAS Catalog

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    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

    Clone Names

    • DKFZp564K247

    Gene Ontology Provided by GOA

    Process Evidence Code Pubs
    involved_in mitochondrial respirasome assembly IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in negative regulation of apoptotic process IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within negative regulation of apoptotic process IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in mitochondrial inner membrane TAS
    Traceable Author Statement
    more info
    		  
    located_in mitochondrion HTP PubMed 
    is_active_in mitochondrion IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in mitochondrion IDA
    Inferred from Direct Assay
    more info
    		  
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
    		  
    part_of protein-containing complex IDA
    Inferred from Direct Assay
    more info
    		  

    General protein information

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    Preferred Names
    HIG1 domain family member 1A, mitochondrial
    Names
    HIG1 domain family, member 1A
    RCF1 homolog A
    hypoxia inducible gene 1
    hypoxia-inducible gene 1 protein

    NCBI Reference Sequences (RefSeq)

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    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_001099668.2 → NP_001093138.1  HIG1 domain family member 1A, mitochondrial isoform a

      See identical proteins and their annotated locations for NP_001093138.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longer isoform (a).
      Source sequence(s)
      AC099329, BC070277, BM983292, BM983580, BP208784, DA428926
      Consensus CDS
      CCDS46806.1
      UniProtKB/TrEMBL
      B2R4G1
      Related
      ENSP00000398064.2, ENST00000452906.3
      Conserved Domains (1) summary
      pfam04588
      Location:42 → 92
      HIG_1_N; Hypoxia induced protein conserved region

    2. NM_001099669.2 → NP_001093139.1  HIG1 domain family member 1A, mitochondrial isoform b

      See identical proteins and their annotated locations for NP_001093139.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) contains a distinct 5' UTR and lacks a portion of the 5' coding region, compared to variant 1. These differences cause translation initiation at a downstream AUG and a protein (isoform b) with a shorter N-terminus compared to isoform a. Both variants 2 and 3 encode the same protein.
      Source sequence(s)
      AC099329, BC070277, BG708126, BM983292, BM983580, BP370118
      Consensus CDS
      CCDS43073.1
      UniProtKB/Swiss-Prot
      Q9UFZ2, Q9Y241
      UniProtKB/TrEMBL
      B2R4G1
      Related
      ENSP00000402160.2, ENST00000418900.6
      Conserved Domains (1) summary
      pfam04588
      Location:28 → 78
      HIG_1_N; Hypoxia induced protein conserved region

    3. NM_014056.4 → NP_054775.2  HIG1 domain family member 1A, mitochondrial isoform b

      See identical proteins and their annotated locations for NP_054775.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) contains a distinct 5' UTR and lacks a portion of the 5' coding region, compared to variant 1. These differences cause translation initiation at a downstream AUG and a protein (isoform b) with a shorter N-terminus compared to isoform a. Both variants 2 and 3 encode the same protein.
      Source sequence(s)
      AC099329, BC070277, BG708126, BM983292, BM983580
      Consensus CDS
      CCDS43073.1
      UniProtKB/Swiss-Prot
      Q9UFZ2, Q9Y241
      UniProtKB/TrEMBL
      B2R4G1
      Related
      ENSP00000319393.7, ENST00000321331.12
      Conserved Domains (1) summary
      pfam04588
      Location:28 → 78
      HIG_1_N; Hypoxia induced protein conserved region

    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

    1. NC_000003.12 Reference GRCh38.p14 Primary Assembly

      Range
      42782908..42804490 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060927.1 Alternate T2T-CHM13v2.0

      Range
      42800951..42820082 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9Y241.1 GenPept UniProtKB/Swiss-Prot:Q9Y241

    Gene LinkOut

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

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