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HCCS Gene(Protein Coding)

Holocytochrome C Synthase

GCID:
GC0XP011129
GIFtS:
47
Genes Participants
UDN Logo

Aliases for HCCS Gene

Aliases for HCCS Gene

  • Holocytochrome C Synthase 2 3 5
  • Microphthalamia With Linear Skin Defects 2 3
  • Holocytochrome C-Type Synthase 3 4
  • Cytochrome C Heme-Lyase 2 3
  • CCHL 3 4
  • Holocytochrome C Synthase (Cytochrome C Heme-Lyase) 2
  • Cytochrome C-Type Heme Lyase 3
  • EC 4.4.1.17 4
  • LSDMCA1 3
  • MCOPS7 3
  • MLS 3

External Ids for HCCS Gene

Previous HGNC Symbols for HCCS Gene

  • MLS

Previous GeneCards Identifiers for HCCS Gene

  • GC0XP010108
  • GC0XP009895
  • GC0XP010425
  • GC0XP010490
  • GC0XP010889
  • GC0XP011039
  • GC0XP008910

Summaries for HCCS Gene

Entrez Gene Summary for HCCS Gene

  • The protein encoded by this gene is an enzyme that covalently links a heme group to the apoprotein of cytochrome c. Defects in this gene are a cause of microphthalmia syndromic type 7 (MCOPS7). Three transcript variants encoding the same protein have been found for this gene. [provided by RefSeq, Jan 2010]

GeneCards Summary for HCCS Gene

HCCS (Holocytochrome C Synthase) is a Protein Coding gene. Diseases associated with HCCS include Linear Skin Defects With Multiple Congenital Anomalies 1 and Sclerocornea. Among its related pathways are Porphyrin and chlorophyll metabolism. Gene Ontology (GO) annotations related to this gene include holocytochrome-c synthase activity.

UniProtKB/Swiss-Prot for HCCS Gene

  • Links covalently the heme group to the apoprotein of cytochrome c.

Gene Wiki entry for HCCS Gene

Additional gene information for HCCS Gene

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

Genomics for HCCS Gene

Products:

  1. Regulatory Element

GeneHancer (GH) Regulatory Elements for HCCS Gene

Promoters and enhancers for HCCS Gene
GeneHancer (GH) Identifier GH Type GH
Score		 GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites		 Gene Targets
GH0XJ011110 Promoter/Enhancer 2.1 EPDnew FANTOM5 Ensembl ENCODE 654.1 +1.1 1136 4.2 PKNOX1 SMAD1 ATF1 ARNT ARID4B SIN3A ZNF48 YY1 POLR2B ELK1 HCCS ENSG00000234129 MID1 ENSG00000207151 GC0XM011116
GH0XJ011340 Enhancer 1.6 FANTOM5 Ensembl ENCODE dbSUPER 3.1 +230.7 230700 2.4 FOXA2 SMAD1 ATF1 ARNT NCOA2 YY1 TCF12 ATF7 RUNX3 RXRA HCCS MSL3 LOC100422628 GC0XM011637 ARHGAP6
GH0XJ011140 Enhancer 0.2 FANTOM5 13.4 +29.0 29027 0.3 ENSG00000207151 ENSG00000234129 HCCS ARHGAP6 ENSG00000278218 GC0XM011122 GC0XM011124
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around HCCS on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the HCCS gene promoter:
  • MEF-2A
  • aMEF-2
  • PPAR-gamma2
  • PPAR-gamma1
  • AREB6
  • GATA-6
  • FOXD3
  • HNF-3beta
  • POU2F1
  • POU2F1a

Genomic Locations for HCCS Gene

Genomic Locations for HCCS Gene
chrX:11,111,286-11,123,086
(GRCh38/hg38)
Size:
11,801 bases
Orientation:
Plus strand
chrX:11,129,406-11,141,206
(GRCh37/hg19)
Size:
11,801 bases
Orientation:
Plus strand

Genomic View for HCCS Gene

Genes around HCCS on UCSC Golden Path with GeneCards custom track

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

RefSeq DNA sequence for HCCS Gene

Proteins for HCCS Gene

Products:

  1. Antibody
  2. Protein
  3. Assay

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

    Protein Symbol:
    P53701-CCHL_HUMAN
    Recommended name:
    Cytochrome c-type heme lyase
    Protein Accession:
    P53701
    Secondary Accessions:
    • B3KUS1
    • Q502X8

    Protein attributes for HCCS Gene

    Size:
    268 amino acids
    Molecular mass:
    30602 Da
    Quaternary structure:
    No Data Available

neXtProt entry for HCCS Gene

Protein Expression for HCCS Gene

See protein expression from ProteomicsDB, MOPED, PaxDb, and MaxQB

Post-translational modifications for HCCS Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for HCCS Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for HCCS Gene

Domains & Families for HCCS Gene

Gene Families for HCCS Gene

Human Protein Atlas (HPA):
  • Disease related genes
  • Enzymes
  • Potential drug targets
  • Predicted secreted proteins

Protein Domains for HCCS Gene

Blocks:
InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for HCCS Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

P53701

UniProtKB/Swiss-Prot:

CCHL_HUMAN :
  • Belongs to the cytochrome c-type heme lyase family.
Family:
  • Belongs to the cytochrome c-type heme lyase family.
genes like me logo Genes that share domains with HCCS: view

Function for HCCS Gene

Products:

  1. Animal Model
  2. CRISPR
  3. miRNA
  4. Inhibitory RNA
  5. Clone
  6. Cell Line

Molecular function for HCCS Gene

UniProtKB/Swiss-Prot Function:
Links covalently the heme group to the apoprotein of cytochrome c.
UniProtKB/Swiss-Prot CatalyticActivity:
Holocytochrome c = apocytochrome c + heme.
GENATLAS Biochemistry:
holocytochrome C-type synthetase,putatively involved in electron transport pathway

Enzyme Numbers (IUBMB) for HCCS Gene

Phenotypes From GWAS Catalog for HCCS Gene

Gene Ontology (GO) - Molecular Function for HCCS Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004408 holocytochrome-c synthase activity IBA --
GO:0016829 lyase activity IEA --
GO:0046872 metal ion binding IEA --
genes like me logo Genes that share ontologies with HCCS: view
genes like me logo Genes that share phenotypes with HCCS: view

Human Phenotype Ontology for HCCS Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for HCCS

Clone Products

No data available for Animal Models , Transcription Factor Targets and HOMER Transcription for HCCS Gene

Localization for HCCS Gene

Subcellular locations from UniProtKB/Swiss-Prot for HCCS Gene

Mitochondrion inner membrane. Membrane; Lipid-anchor.

Subcellular locations from

COMPARTMENTS
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 HCCS gene
Compartment Confidence
mitochondrion 5
plasma membrane 2
extracellular 2
nucleus 2
cytosol 2
cytoskeleton 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Mitochondria (4)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for HCCS Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005739 mitochondrion IDA 11827457
GO:0005743 mitochondrial inner membrane TAS,IEA --
GO:0016020 membrane IEA --
genes like me logo Genes that share ontologies with HCCS: view

Pathways & Interactions for HCCS Gene

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

Pathways by source for HCCS Gene

1 KEGG pathway for HCCS Gene

Gene Ontology (GO) - Biological Process for HCCS Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0009887 animal organ morphogenesis TAS 8661044
GO:0018063 cytochrome c-heme linkage IBA --
GO:0055114 oxidation-reduction process TAS 8661044
genes like me logo Genes that share ontologies with HCCS: view

No data available for SIGNOR curated interactions for HCCS Gene

Drugs & Compounds for HCCS Gene

Products:

  1. Drug

(1) Drugs for HCCS Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
heme Pharma Agonist 0
genes like me logo Genes that share compounds with HCCS: view

Transcripts for HCCS Gene

Products:

  1. CRISPR
  2. miRNA
  3. Inhibitory RNA
  4. Clone

mRNA/cDNA for HCCS Gene

(4) REFSEQ mRNAs :
(6) Additional mRNA sequences :
(142) Selected AceView cDNA sequences:
(3) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for HCCS Gene

Holocytochrome c synthase:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for HCCS

Clone Products

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

ExUns: 1a · 1b · 1c · 1d ^ 2a · 2b ^ 3 ^ 4a · 4b ^ 5a · 5b ^ 6 ^ 7a · 7b · 7c
SP1: - - - -
SP2: - - -
SP3: - -
SP4: -
SP5:

Relevant External Links for HCCS Gene

GeneLoc Exon Structure for
HCCS
ECgene alternative splicing isoforms for
HCCS

Expression for HCCS Gene

Products:

  1. Primer
  2. Gene Expression Assay

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

mRNA expression in normal human tissues for HCCS Gene
mRNA expression by GTEx for HCCS GenemRNA expression by BioGPS for HCCS Gene

Protein differential expression in normal tissues from HIPED for HCCS Gene

This gene is overexpressed in Bone (43.6) and Breast (16.6).

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



Protein tissue co-expression partners for HCCS Gene

NURSA nuclear receptor signaling pathways regulating expression of HCCS Gene:

HCCS

SOURCE GeneReport for Unigene cluster for HCCS Gene:

Hs.211571

Evidence on tissue expression from TISSUES for HCCS Gene

  • Nervous system(4.6)
  • Spleen(3)
  • Blood(2.9)
  • Heart(2.6)
  • Lymph node(2.5)
  • Muscle(2.4)
  • Skin(2.4)
  • Liver(2.3)
  • Bone marrow(2.2)
  • Intestine(2.2)
  • Kidney(2.1)
  • Lung(2.1)

Phenotype-based relationships between genes and organs from Gene ORGANizer for HCCS Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
Systems:
  • cardiovascular
  • digestive
  • integumentary
  • nervous
  • reproductive
  • respiratory
  • skeletal muscle
  • skeleton
  • urinary
Regions:
Head and neck:
  • brain
  • cerebellum
  • cerebrospinal fluid
  • chin
  • cranial nerve
  • ear
  • eye
  • face
  • head
  • jaw
  • lacrimal apparatus
  • mandible
  • maxilla
  • meninges
  • mouth
  • nose
  • scalp
  • skull
Thorax:
  • aorta
  • chest wall
  • diaphragm
  • heart
  • heart valve
  • lung
Abdomen:
  • abdominal wall
  • intestine
  • large intestine
  • liver
  • small intestine
  • stomach
Pelvis:
  • anus
  • ovary
  • penis
  • rectum
  • testicle
  • urethra
  • uterus
  • vagina
General:
  • blood
  • blood vessel
  • hair
  • peripheral nervous system
  • skin
genes like me logo Genes that share expression patterns with HCCS: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues and mRNA Expression by UniProt/SwissProt for HCCS Gene

Orthologs for HCCS Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for HCCS Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
 Mammalia HCCS 34
  • 100 (a)
 OneToOne
LOC465489 33
  • 91.92 (n)
dog
(Canis familiaris)
 Mammalia HCCS 34 33
  • 87.19 (n)
 OneToOne
rat
(Rattus norvegicus)
 Mammalia Hccs 33
  • 85.82 (n)
mouse
(Mus musculus)
 Mammalia Hccs 16 34 33
  • 85.2 (n)
cow
(Bos Taurus)
 Mammalia HCCS 34 33
  • 84.95 (n)
 OneToOne
oppossum
(Monodelphis domestica)
 Mammalia HCCS 34
  • 82 (a)
 OneToOne
platypus
(Ornithorhynchus anatinus)
 Mammalia HCCS 34
  • 76 (a)
 OneToOne
chicken
(Gallus gallus)
 Aves HCCS 34 33
  • 75.41 (n)
 OneToOne
lizard
(Anolis carolinensis)
 Reptilia HCCS 34
  • 68 (a)
 OneToOne
tropical clawed frog
(Silurana tropicalis)
 Amphibia hccs 33
  • 69.72 (n)
Str.5948 33
African clawed frog
(Xenopus laevis)
 Amphibia hccs-prov 33
zebrafish
(Danio rerio)
 Actinopterygii hccs 34 33
  • 67.05 (n)
 OneToMany
hccsa 34
  • 63 (a)
 OneToMany
hccsal 34
  • 60 (a)
 OneToMany
Dr.4423 33
rainbow trout
(Oncorhynchus mykiss)
 Actinopterygii Omy.12440 33
fruit fly
(Drosophila melanogaster)
 Insecta CG6022 35
  • 53 (a)
Cchl 34
  • 52 (a)
 OneToOne
worm
(Caenorhabditis elegans)
 Secernentea T06D8.6 35
  • 58 (a)
cchl-1 34
  • 47 (a)
 OneToOne
K. lactis yeast
(Kluyveromyces lactis)
 Saccharomycetes KLLA0F25894g 33
  • 53.98 (n)
baker's yeast
(Saccharomyces cerevisiae)
 Saccharomycetes CYT2 34 33
  • 51.39 (n)
 OneToOne
CYC3 36 36
A. gosspyii yeast
(Ashbya gossypii)
 Saccharomycetes AGOS_ADR154W 33
  • 51.07 (n)
fission yeast
(Schizosaccharomyces pombe)
 Schizosaccharomycetes SPAC24C9.02c 33
  • 53.14 (n)
sea squirt
(Ciona savignyi)
 Ascidiacea CSA.4216 34
  • 53 (a)
 OneToOne
Cin.4806 33
bread mold
(Neurospora crassa)
 Ascomycetes NCU08138 33
  • 50.52 (n)
sea squirt
(Ciona intestinalis)
 Ascidiacea Cin.4806 33
Species where no ortholog for HCCS was found in the sources mined by GeneCards:
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • 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 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)

Evolution for HCCS Gene

ENSEMBL:
Gene Tree for HCCS (if available)
TreeFam:
Gene Tree for HCCS (if available)
Aminode:
Evolutionary constrained regions (ECRs) for HCCS: view image

Paralogs for HCCS Gene

(1) SIMAP similar genes for HCCS Gene using alignment to 1 proteins:

  • CCHL_HUMAN
genes like me logo Genes that share paralogs with HCCS: view

No data available for Paralogs for HCCS Gene

Variants for HCCS Gene

Products:

  1. SNP Genotyping and Copy Number Assay

Sequence variations from dbSNP and Humsavar for HCCS Gene

SNP ID Clin Chr 0X pos Variation AA Info Type
rs121917888 pathogenic, Linear skin defects with multiple congenital anomalies 1 11,120,974(+) C/T coding_sequence_variant, stop_gained
rs121917889 pathogenic, Linear skin defects with multiple congenital anomalies 1, Linear skin defects with multiple congenital anomalies 1 (LSDMCA1) [MIM:309801] 11,121,652(+) C/T coding_sequence_variant, missense_variant
rs144641429 uncertain-significance, benign, not provided, not specified 11,112,065(+) G/A coding_sequence_variant, missense_variant
rs193929392 pathogenic, Linear skin defects with multiple congenital anomalies 1 11,118,574(+) G/A coding_sequence_variant, missense_variant
rs2070163 conflicting-interpretations-of-pathogenicity, not specified 11,114,949(+) C/T coding_sequence_variant, missense_variant

Variation tolerance for HCCS Gene

Residual Variation Intolerance Score: 84.6% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.60; 12.87% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for HCCS Gene

Human Gene Mutation Database (HGMD)
HCCS
SNPedia medical, phenotypic, and genealogical associations of SNPs for
HCCS

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Structural Variations from Database of Genomic Variants (DGV) for HCCS Gene

Disorders for HCCS Gene

MalaCards: The human disease database

(24) MalaCards diseases for HCCS Gene - From: HGMD, OMIM, ClinVar, GTR, Orphanet, Swiss-Prot, DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
linear skin defects with multiple congenital anomalies 1
  • lsdmca1
sclerocornea
  • isolated congenital sclerocornea
brain compression
  • compression of brain
mansonelliasis
  • mansonella perstans infections
heel spur
  • calcaneal spur
- elite association - COSMIC cancer census association via MalaCards
Search HCCS in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

CCHL_HUMAN
  • Linear skin defects with multiple congenital anomalies 1 (LSDMCA1) [MIM:309801]: A disorder characterized by dermal, ocular, neurological and cardiac abnormalities. LSDMCA1 main features are unilateral or bilateral microphthalmia, linear skin defects in affected females, and in utero lethality for males. Skin defects are limited to the face and neck, consisting of areas of aplastic skin that heal with age to form hyperpigmented areas. Additional features in female patients include agenesis of the corpus callosum, sclerocornea, chorioretinal abnormalities, infantile seizures, congenital heart defect, mental retardation, and diaphragmatic hernia. Microphthalmia is a disorder of eye formation, ranging from small size of a single eye to complete bilateral absence of ocular tissues (anophthalmia). In many cases, microphthalmia/anophthalmia occurs in association with syndromes that include non-ocular abnormalities. {ECO:0000269 PubMed:17033964}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Additional Disease Information for HCCS

Genetic Association Database
(GAD)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with HCCS: view

No data available for Genatlas for HCCS Gene

Publications for HCCS Gene

  1. Mutations of the mitochondrial holocytochrome c-type synthase in X-linked dominant microphthalmia with linear skin defects syndrome. (PMID: 17033964) Wimplinger I … Kutsche K (American journal of human genetics 2006) 3 4 22 58
  2. Genomic structure of a human holocytochrome c-type synthetase gene in Xp22.3 and mutation analysis in patients with Rett syndrome. (PMID: 9674913) Van den Veyver IB … Zoghbi HY (American journal of medical genetics 1998) 3 4 22 58
  3. Cloning and characterization of a putative human holocytochrome c-type synthetase gene (HCCS) isolated from the critical region for microphthalmia with linear skin defects (MLS). (PMID: 8661044) Schaefer L … Zoghbi HY (Genomics 1996) 3 4 22 58
  4. A genome-wide study of common SNPs and CNVs in cognitive performance in the CANTAB. (PMID: 19734545) Need AC … Goldstein DB (Human molecular genetics 2009) 3 44 58
  5. HCCS loss-of-function missense mutation in a female with bilateral microphthalmia and sclerocornea: a novel gene for severe ocular malformations? (PMID: 17893649) Wimplinger I … Kutsche K (Molecular vision 2007) 3 22 58

Products for HCCS Gene

Sources for HCCS Gene

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