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Aliases for HIGD1A Gene

Aliases for HIGD1A Gene

  • HIG1 Hypoxia Inducible Domain Family Member 1A 2 3 5
  • Hypoxia-Inducible Gene 1 Protein 3 4
  • HIG1 Domain Family, Member 1A 2 3
  • Hypoxia Inducible Gene 1 2 3
  • RCF1 Homolog A 3 4
  • RCF1a 3 4
  • HIG1 3 4
  • HIG1 Hypoxia Inducible Domain Family, Member 1A 2
  • HIG1 Domain Family Member 1A, Mitochondrial 3

External Ids for HIGD1A Gene

Summaries for HIGD1A Gene

GeneCards Summary for HIGD1A Gene

HIGD1A (HIG1 Hypoxia Inducible Domain Family Member 1A) is a Protein Coding gene. Diseases associated with HIGD1A include Hypoxia. Among its related pathways are CDK-mediated phosphorylation and removal of Cdc6 and Cellular Senescence (REACTOME). An important paralog of this gene is ENSG00000280571.

UniProtKB/Swiss-Prot for HIGD1A Gene

  • Proposed subunit of cytochrome c oxidase (COX, complex IV), which is the terminal component of the mitochondrial respiratory chain that catalyzes the reduction of oxygen to water. May play a role in the assembly of respiratory supercomplexes.

Gene Wiki entry for HIGD1A Gene

Additional gene information for HIGD1A Gene

No data available for Entrez Gene Summary , CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for HIGD1A Gene

Genomics for HIGD1A Gene

GeneHancer (GH) Regulatory Elements for HIGD1A Gene

Promoters and enhancers for HIGD1A Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH03J042802 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 650.7 +0.4 411 3.1 HDGF PKNOX1 FOXA2 MLX ARNT ZFP64 ARID4B SIN3A FEZF1 DMAP1 ACKR2 ENSG00000280571 HIGD1A NKTR ZNF662 RN7SL567P GEMIN2P2 RPL36P20 SNRK-AS1 CCDC13
GH03J042880 Enhancer 1.5 FANTOM5 Ensembl ENCODE 15 -76.5 -76505 1.3 PKNOX1 ATF1 ARID4B SIN3A DMAP1 ZNF2 ZNF48 YY1 ETS1 GLIS2 NKTR HIGD1A SNRK-AS1 ENSG00000235288 ACKR2 ZNF662 CCDC13 LINC02158 KRBOX1 CYP8B1
GH03J042772 Promoter/Enhancer 1.9 EPDnew Ensembl ENCODE 9.5 +31.4 31385 1.4 PKNOX1 ATF1 SMAD1 SIN3A BMI1 IRF4 RFX5 YY1 ZNF207 ZNF143 CCDC13 CCDC13-AS1 HIGD1A LINC02158 ENSG00000280571
GH03J042778 Enhancer 0.8 Ensembl ENCODE 20.5 +25.3 25348 1.8 FOXA2 RXRA MAX RAD21 YY1 SP1 JUND ATF3 EGR1 ZBTB33 HIGD1A CCDC13-AS1 ACKR2 KRBOX1 CCDC13 GC03P042799 ENSG00000280571
GH03J042759 Enhancer 1.2 Ensembl ENCODE dbSUPER 9.5 +42.9 42913 3.6 ZFP64 RARA YY1 ATF7 THAP11 RXRA CEBPB ZNF518A ZNF781 SP1 CCDC13-AS1 SEC22C POMGNT2 HIGD1A LINC02158 CCDC13 ENSG00000280571
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around HIGD1A on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the HIGD1A gene promoter:
  • LyF-1
  • Meis-1b
  • HOXA9
  • HOXA9B
  • Meis-1

Genomic Locations for HIGD1A Gene

Genomic Locations for HIGD1A Gene
21,628 bases
Minus strand
47,359 bases
Minus strand

Genomic View for HIGD1A Gene

Genes around HIGD1A on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
HIGD1A Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for HIGD1A Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for HIGD1A Gene

Proteins for HIGD1A Gene

  • Protein details for HIGD1A Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    HIG1 domain family member 1A, mitochondrial
    Protein Accession:
    Secondary Accessions:
    • Q9UFZ2

    Protein attributes for HIGD1A Gene

    93 amino acids
    Molecular mass:
    10143 Da
    Quaternary structure:
    • Associates with cytochrome c oxidase (COX, complex IV); proposed complex component. Also associates with respiratory chain supercomplexes.
    • Sequence=BG400624; Type=Frameshift; Positions=32; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for HIGD1A Gene

    Alternative splice isoforms for HIGD1A Gene


neXtProt entry for HIGD1A Gene

Post-translational modifications for HIGD1A Gene

  • Ubiquitination at Lys19
  • Modification sites at PhosphoSitePlus

Other Protein References for HIGD1A Gene

No data available for DME Specific Peptides for HIGD1A Gene

Domains & Families for HIGD1A Gene

Gene Families for HIGD1A Gene

Human Protein Atlas (HPA):
  • Predicted membrane proteins

Protein Domains for HIGD1A Gene


Suggested Antigen Peptide Sequences for HIGD1A Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with HIGD1A: view

No data available for UniProtKB/Swiss-Prot for HIGD1A Gene

Function for HIGD1A Gene

Molecular function for HIGD1A Gene

UniProtKB/Swiss-Prot Function:
Proposed subunit of cytochrome c oxidase (COX, complex IV), which is the terminal component of the mitochondrial respiratory chain that catalyzes the reduction of oxygen to water. May play a role in the assembly of respiratory supercomplexes.
UniProtKB/Swiss-Prot Induction:
By hypoxia.

Phenotypes From GWAS Catalog for HIGD1A Gene

genes like me logo Genes that share phenotypes with HIGD1A: view

Animal Model Products

Clone Products

No data available for Enzyme Numbers (IUBMB) , Gene Ontology (GO) - Molecular Function , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for HIGD1A Gene

Localization for HIGD1A Gene

Subcellular locations from UniProtKB/Swiss-Prot for HIGD1A Gene

Mitochondrion membrane; Multi-pass membrane protein. Mitochondrion inner membrane.

Subcellular locations from

Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for HIGD1A gene
Compartment Confidence
mitochondrion 5
nucleus 5
cytosol 2
extracellular 1
peroxisome 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Mitochondria (3)
  • Nucleoplasm (3)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for HIGD1A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005654 nucleoplasm IDA --
GO:0005739 mitochondrion IEA,IDA --
GO:0005743 mitochondrial inner membrane TAS --
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
genes like me logo Genes that share ontologies with HIGD1A: view

Pathways & Interactions for HIGD1A Gene

genes like me logo Genes that share pathways with HIGD1A: view

Gene Ontology (GO) - Biological Process for HIGD1A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0043066 negative regulation of apoptotic process IDA 21856340
GO:0055114 oxidation-reduction process IEA --
GO:0061418 regulation of transcription from RNA polymerase II promoter in response to hypoxia TAS --
genes like me logo Genes that share ontologies with HIGD1A: view

No data available for SIGNOR curated interactions for HIGD1A Gene

Drugs & Compounds for HIGD1A Gene

No Compound Related Data Available

Transcripts for HIGD1A Gene

mRNA/cDNA for HIGD1A Gene

Unigene Clusters for HIGD1A Gene

HIG1 hypoxia inducible domain family, member 1A:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for HIGD1A Gene

ExUns: 1a · 1b · 1c · 1d · 1e ^ 2 ^ 3a · 3b ^ 4a · 4b ^ 5a · 5b ^ 6a · 6b
SP1: - - - - -
SP2: - -
SP3: - - -
SP4: - - - - - -
SP5: - - - -
SP6: - -

Relevant External Links for HIGD1A Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for HIGD1A Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for HIGD1A Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for HIGD1A Gene

This gene is overexpressed in Bone (9.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for HIGD1A Gene

Protein tissue co-expression partners for HIGD1A Gene

NURSA nuclear receptor signaling pathways regulating expression of HIGD1A Gene:


SOURCE GeneReport for Unigene cluster for HIGD1A Gene:


Evidence on tissue expression from TISSUES for HIGD1A Gene

  • Nervous system(5)
  • Lung(4.8)
  • Skin(4.7)
  • Kidney(4.4)
  • Blood(4.2)
  • Bone marrow(4.1)
  • Muscle(3.9)
  • Intestine(3.3)
  • Liver(2.9)
  • Eye(2.2)
genes like me logo Genes that share expression patterns with HIGD1A: view

No data available for mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for HIGD1A Gene

Orthologs for HIGD1A Gene

This gene was present in the common ancestor of animals.

Orthologs for HIGD1A Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia HIGD1A 33
  • 99.07 (n)
-- 34
  • 99 (a)
-- 34
  • 99 (a)
(Canis familiaris)
Mammalia HIGD1A 34 33
  • 89.96 (n)
(Bos Taurus)
Mammalia HIGD1A 33
  • 89.61 (n)
HIGD1D 34 34 34
  • 84 (a)
-- 34
  • 83 (a)
-- 34
  • 83 (a)
-- 34
  • 82 (a)
(Mus musculus)
Mammalia Higd1a 16 34 33
  • 83.51 (n)
Gm9790 34
  • 83 (a)
(Monodelphis domestica)
Mammalia -- 34
  • 83 (a)
-- 34
  • 77 (a)
(Rattus norvegicus)
Mammalia Higd1a 33
  • 82.08 (n)
(Ornithorhynchus anatinus)
Mammalia HIGD1A 34
  • 81 (a)
(Gallus gallus)
Aves HIGD1A 33
  • 66.3 (n)
(Anolis carolinensis)
Reptilia -- 34
  • 75 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia higd1a 33
  • 69.23 (n)
(Danio rerio)
Actinopterygii hig1 34 33
  • 65.81 (n)
-- 33
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.9500 33
fruit fly
(Drosophila melanogaster)
Insecta CG11825 34
  • 31 (a)
Species where no ortholog for HIGD1A was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for HIGD1A Gene

Gene Tree for HIGD1A (if available)
Gene Tree for HIGD1A (if available)
Evolutionary constrained regions (ECRs) for HIGD1A: view image

Paralogs for HIGD1A Gene

Paralogs for HIGD1A Gene

(4) SIMAP similar genes for HIGD1A Gene using alignment to 3 proteins:

genes like me logo Genes that share paralogs with HIGD1A: view

Variants for HIGD1A Gene

Sequence variations from dbSNP and Humsavar for HIGD1A Gene

SNP ID Clin Chr 03 pos Variation AA Info Type
rs1000351039 -- 42,802,007(-) G/T intron_variant
rs1000407274 -- 42,803,636(-) G/A intron_variant
rs1000608613 -- 42,786,089(-) G/A coding_sequence_variant, synonymous_variant
rs1000960089 -- 42,803,953(-) C/T intron_variant
rs1001175236 -- 42,795,787(-) G/A intron_variant

Structural Variations from Database of Genomic Variants (DGV) for HIGD1A Gene

Variant ID Type Subtype PubMed ID
dgv2514n106 CNV deletion 24896259
esv1004289 CNV deletion 20482838
esv1232041 CNV deletion 17803354
esv2725200 CNV deletion 23290073
esv2837013 CNV deletion 24192839
esv3561797 CNV deletion 23714750
esv4812 CNV loss 18987735
esv6998 CNV loss 19470904
nsv1072683 CNV deletion 25765185
nsv1129057 CNV deletion 24896259
nsv1139109 CNV deletion 24896259
nsv1146148 CNV deletion 26484159
nsv236207 CNV deletion 16902084
nsv435763 CNV deletion 17901297
nsv513043 CNV loss 21212237
nsv955515 CNV deletion 24416366
nsv979823 CNV duplication 23825009

Variation tolerance for HIGD1A Gene

Residual Variation Intolerance Score: 68.6% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.49; 10.62% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for HIGD1A Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for HIGD1A Gene

Disorders for HIGD1A Gene

MalaCards: The human disease database

(1) MalaCards diseases for HIGD1A Gene - From: GeneCards

Disorder Aliases PubMed IDs
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for HIGD1A

Genetic Association Database
Human Genome Epidemiology Navigator
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with HIGD1A: view

No data available for UniProtKB/Swiss-Prot and Genatlas for HIGD1A Gene

Publications for HIGD1A Gene

  1. Rcf1 mediates cytochrome oxidase assembly and respirasome formation, revealing heterogeneity of the enzyme complex. (PMID: 22342701) Vukotic M … Deckers M (Cell metabolism 2012) 2 3 4 58
  2. Higd1a is a positive regulator of cytochrome c oxidase. (PMID: 25605899) Hayashi T … Takashima S (Proceedings of the National Academy of Sciences of the United States of America 2015) 2 3 58
  3. Genetic variants in nuclear-encoded mitochondrial genes influence AIDS progression. (PMID: 20877624) Hendrickson SL … O'Brien SJ (PloS one 2010) 3 44 58
  4. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 58
  5. Toward a catalog of human genes and proteins: sequencing and analysis of 500 novel complete protein coding human cDNAs. (PMID: 11230166) Wiemann S … Poustka A (Genome research 2001) 3 4 58

Products for HIGD1A Gene

Sources for HIGD1A Gene

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