Human Gene HCCS (uc004cuj.3) Description and Page Index
  Description: Homo sapiens holocytochrome c synthase (HCCS), transcript variant 2, mRNA.
RefSeq Summary (NM_001122608): 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].
Transcript (Including UTRs)
   Position: hg19 chrX:11,129,406-11,141,204 Size: 11,799 Total Exon Count: 7 Strand: +
Coding Region
   Position: hg19 chrX:11,130,181-11,139,930 Size: 9,750 Coding Exon Count: 6 

Page IndexSequence and LinksUniProtKB CommentsGenetic AssociationsMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesGeneReviewsModel Information
Methods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chrX:11,129,406-11,141,204)mRNA (may differ from genome)Protein (268 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCLynxMGIneXtProt
OMIMPubMedStanford SOURCETreefamUniProtKBWikipedia

-  Comments and Description Text from UniProtKB
  ID: CCHL_HUMAN
DESCRIPTION: RecName: Full=Cytochrome c-type heme lyase; Short=CCHL; EC=4.4.1.17; AltName: Full=Holocytochrome c-type synthase;
FUNCTION: Links covalently the heme group to the apoprotein of cytochrome c (By similarity).
CATALYTIC ACTIVITY: Holocytochrome c = apocytochrome c + heme.
SUBCELLULAR LOCATION: Mitochondrion inner membrane (Potential).
DISEASE: Defects in HCCS are a cause of microphthalmia syndromic type 7 (MCOPS7) [MIM:309801]; also known as microphthalmia with linear skin defects (MLS) or MIDAS syndrome. Microphthalmia is a clinically heterogeneous 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. MCOPS7 is a disorder characterized by 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.
SIMILARITY: Belongs to the cytochrome c-type heme lyase family.
SIMILARITY: Contains 2 HRM (heme regulatory motif) repeats.
WEB RESOURCE: Name=GeneReviews; URL="http://www.ncbi.nlm.nih.gov/sites/GeneTests/lab/gene/HCCS";

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): HCCS
CDC HuGE Published Literature: HCCS
Positive Disease Associations: Cognitive performance
Related Studies:
  1. Cognitive performance
    Need ,et al. 2009, A Genome-wide Study of Common SNPs and CNVs in Cognitive Performance in the CANTAB battery, Human molecular genetics 2009 18- 23 : 4650-61. [PubMed 19734545]

-  MalaCards Disease Associations
  MalaCards Gene Search: HCCS
Diseases sorted by gene-association score: linear skin defects with multiple congenital anomalies 1* (1680), sclerocornea (35), microphthalmia (20), brain compression (16), mansonelliasis (16), heel spur (15), osteogenesis imperfecta, type xi (11), type 1 diabetes mellitus 10 (11), diabetes mellitus, insulin-dependent, 15 (10), conjunctival nevus (10), choreoacanthocytosis (9), diabetes mellitus, insulin-dependent, 3 (7), focal dermal hypoplasia (7), bladder neck obstruction (7), acute maxillary sinusitis (7), shoulder impingement syndrome (7), malignant granular cell myoblastoma (6), hemopneumothorax (6), diabetes mellitus, insulin-dependent, 5 (6), myxoid liposarcoma (5), diabetes mellitus, insulin-dependent, 6 (5), leukodystrophy, hypomyelinating, 2 (4), tyrosinemia, type ii (3)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 15.02 RPKM in Heart - Left Ventricle
Total median expression: 358.45 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -88.50217-0.408 Picture PostScript Text
3' UTR -296.991274-0.233 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR000511 - Cyt_C/C1_haem_lyase

Pfam Domains:
PF01265 - Cytochrome c/c1 heme lyase

ModBase Predicted Comparative 3D Structure on P53701
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologGenome BrowserGenome BrowserGenome BrowserGenome Browser
Gene Details  Gene DetailsGene DetailsGene Details
Gene Sorter  Gene SorterGene SorterGene Sorter
  EnsemblFlyBaseWormBaseSGD
  Protein SequenceProtein SequenceProtein SequenceProtein Sequence
  AlignmentAlignmentAlignmentAlignment

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0004408 holocytochrome-c synthase activity
GO:0016829 lyase activity
GO:0046872 metal ion binding

Biological Process:
GO:0009887 animal organ morphogenesis
GO:0018063 cytochrome c-heme linkage
GO:0055114 oxidation-reduction process

Cellular Component:
GO:0005739 mitochondrion
GO:0005743 mitochondrial inner membrane
GO:0016020 membrane


-  Descriptions from all associated GenBank mRNAs
  LF385368 - JP 2014500723-A/192871: Polycomb-Associated Non-Coding RNAs.
LF211733 - JP 2014500723-A/19236: Polycomb-Associated Non-Coding RNAs.
AK097815 - Homo sapiens cDNA FLJ40496 fis, clone TESTI2044788, highly similar to CYTOCHROME C-TYPE HEME LYASE (EC 4.4.1.17).
CR749578 - Homo sapiens mRNA; cDNA DKFZp779I1858 (from clone DKFZp779I1858).
BC095455 - Homo sapiens holocytochrome c synthase (cytochrome c heme-lyase), mRNA (cDNA clone MGC:111231 IMAGE:30512178), complete cds.
MA620945 - JP 2018138019-A/192871: Polycomb-Associated Non-Coding RNAs.
MA447310 - JP 2018138019-A/19236: Polycomb-Associated Non-Coding RNAs.
BC001691 - Homo sapiens holocytochrome c synthase (cytochrome c heme-lyase), mRNA (cDNA clone MGC:1443 IMAGE:3030501), complete cds.
JC506674 - Sequence 42 from Patent EP2733220.
JC737786 - Sequence 42 from Patent WO2014075939.
JC506688 - Sequence 56 from Patent EP2733220.
JC737800 - Sequence 56 from Patent WO2014075939.
JC506661 - Sequence 29 from Patent EP2733220.
JC737773 - Sequence 29 from Patent WO2014075939.
JC506666 - Sequence 34 from Patent EP2733220.
JC737778 - Sequence 34 from Patent WO2014075939.
U36787 - Human putative holocytochrome c-type synthetase mRNA, complete cds.
EU832332 - Synthetic construct Homo sapiens clone HAIB:100067361; DKFZo008F0627 holocytochrome c synthase (cytochrome c heme-lyase) protein (HCCS) gene, encodes complete protein.
EU832417 - Synthetic construct Homo sapiens clone HAIB:100067446; DKFZo004F0628 holocytochrome c synthase (cytochrome c heme-lyase) protein (HCCS) gene, encodes complete protein.
KJ891338 - Synthetic construct Homo sapiens clone ccsbBroadEn_00732 HCCS gene, encodes complete protein.
KR710380 - Synthetic construct Homo sapiens clone CCSBHm_00012080 HCCS (HCCS) mRNA, encodes complete protein.
KR710381 - Synthetic construct Homo sapiens clone CCSBHm_00012082 HCCS (HCCS) mRNA, encodes complete protein.
HQ447225 - Synthetic construct Homo sapiens clone IMAGE:100070527; CCSB006746_04 holocytochrome c synthase (cytochrome c heme-lyase) (HCCS) gene, encodes complete protein.
LF383209 - JP 2014500723-A/190712: Polycomb-Associated Non-Coding RNAs.
LF383206 - JP 2014500723-A/190709: Polycomb-Associated Non-Coding RNAs.
LF383205 - JP 2014500723-A/190708: Polycomb-Associated Non-Coding RNAs.
MA618786 - JP 2018138019-A/190712: Polycomb-Associated Non-Coding RNAs.
MA618783 - JP 2018138019-A/190709: Polycomb-Associated Non-Coding RNAs.
MA618782 - JP 2018138019-A/190708: Polycomb-Associated Non-Coding RNAs.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa00860 - Porphyrin and chlorophyll metabolism

-  Other Names for This Gene
  Alternate Gene Symbols: B3KUS1, CCHL, CCHL_HUMAN, NM_001122608, NP_005324, P53701, Q502X8
UCSC ID: uc004cuj.3
RefSeq Accession: NM_001122608
Protein: P53701 (aka CCHL_HUMAN)
CCDS: CCDS14139.1

-  GeneReviews for This Gene
  GeneReviews article(s) related to gene HCCS:
cdh-ov (Congenital Diaphragmatic Hernia Overview)
microph-lsd (Microphthalmia with Linear Skin Defects Syndrome)

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_001122608.2
exon count: 7CDS single in 3' UTR: no RNA size: 2307
ORF size: 807CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 1814.00frame shift in genome: no % Coverage: 99.61
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.