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Category   Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21
GIFtS

KHDC3L Gene

protein-coding   GIFtS: 39
GCID: GC06P074073

KH domain containing 3-like, subcortical maternal complex...

(Previous name: chromosome 6 open reading frame 221 )
(Previous symbol: C6orf221)
 Explore 1 disease affiliated with
KHDC3L via
MalaCards
our new
 Human Malady Compendium 
Biological research products
for KHDC3L    

Aliases
for KHDC3L gene

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, and/or 10fRNAdb)
About This Section
Aliases
KH Domain Containing 3-Like, Subcortical Maternal Complex Member1 2     Chromosome 6 Open Reading Frame 2211
C6orf2211 2 3 5     HYDM22
ECAT11 2 3 5     KHDC3-Like Protein2
ES Cell-Associated Transcript 1 Protein2 3     

External Ids:    HGNC: 336991   Entrez Gene: 1542882   Ensembl: ENSG000002039087   OMIM: 6116875   UniProtKB: Q587J83   

Export aliases for KHDC3L gene to outside databases


Summaries
for KHDC3L gene

(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section
Entrez Gene summary for KHDC3L:
The protein encoded by this gene belongs to the KHDC1 family, members of which contain an atypical KH domain that may
not bind RNA like canonical KH domains. This gene is specifically expressed in the oocytes, and recent studies suggest
that it may function as a regulator of genomic imprinting in the oocyte. Mutations in this gene are associated with
recurrent biparental complete hydatidiform mole. (provided by RefSeq, Dec 2011)




Genomic Views
for KHDC3L gene

(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 69), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000006.11  NC_018917.1  NT_007299.13  
Regulatory elements:
   Search SABiosciences Regulatory transcription factor binding sites for KHDC3L
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmid: KHDC3L promoter sequence
   Search SABiosciences Chromatin IP Primers for KHDC3L

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat KHDC3L


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 6q13   Ensembl cytogenetic band:  6q13   HGNC cytogenetic band: 6q13

KHDC3L Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
KHDC3L gene location

GeneLoc information about chromosome 6         GeneLoc Exon Structure

GeneLoc location for GC06P074073:  view genomic region     (about GC identifiers)

Start:
 74,072,400 bp from pter      End:
 74,073,898 bp from pter
Size:
 1,499 bases      Orientation:
 plus strand

Proteins
for KHDC3L gene

(According to 1UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to 2PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE MOPED and PaxDb, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, and/or Uscn,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Uscn, Ontologies according to Gene Ontology Consortium 01 Mar 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, and/or Uscn)
About This Section
UniProtKB/Swiss-Prot: KHD3L_HUMAN, Q587J8 (See protein sequence)
Recommended Name: KHDC3-like protein  
Size: 217 amino acids; 24306 Da
Caution: Considered by a number of resources to be the ortholog of rodent Khdc3/Filia. However, sequence similarity is
low and synteny is not conserved. According to PubMed:17913455, KHDC3L/ECAT1 has been lost in rodents
Secondary accessions: B2RNW7

Explore the universe of human proteins at neXtProt for KHDC3L: NX_Q587J8

Post-translational modifications:

  • View modification sites using PhosphoSitePlus2
  • View neXtProt modification sites for NX_Q587J8

    • KHDC3L Protein expression data from MOPED and PaxDb:    About this image 
    Estimated protein expression log10 (pmol).

    REFSEQ proteins: NP_001017361.1  
    ENSEMBL proteins: 
     ENSP00000359392  

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    Uscn Proteins for KHDC3L

    Gene Ontology (GO): 3 cellular component terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005938cell cortex ----
    GO:0043234protein complex IEA--
    GO:0045179apical cortex IEA--


    KHDC3L for ontologies           About GeneDecksing



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    Protein Domains /
    Families
    for KHDC3L gene

    (According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section

    ProtoNet protein and cluster: Q587J8

    UniProtKB/Swiss-Prot: KHD3L_HUMAN, Q587J8
    Domain: Contains an atypical KH domain with amino acid changes at critical sites, suggesting that it may not bind RNA
    Similarity: Belongs to the KHDC1 family
    Similarity: Contains 1 KH domain


    Function
    for KHDC3L gene

    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013,
    bound targets from SABiosciences, miRNA Gene Targets from miRTarBase shRNA from OriGene, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene.)
    About This Section
    miRNA
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    Inhib. RNA
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    In Situ Assay
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    Gene Ontology (GO): 1 molecular function term (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005515protein binding ----


    KHDC3L for ontologies           About GeneDecksing


    1 GenomeRNAi human phenotype for KHDC3L:
     Elongated cells with protrusio 

    Animal Models:
         Mouse knock-out Khdc3tm1Dean for KHDC3L
         2 MGI mutant phenotypes (inferred from 1 allele) (MGI details for Khdc3):
     other  reproductive system 

    KHDC3L for phenotypes           About GeneDecksing


    Pathways & Interactions
    for KHDC3L gene

    (Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to SABiosciences, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene).
    About This Section



    Interactions:

        Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for KHDC3L

    3 Interacting proteins for KHDC3L (Q587J83) via UniProtKB, MINT, STRING, and/or I2D
    InteractantInteraction Details
    GeneCardExternal ID(s)
    NLRP5P590473I2D: score=2 
    OOEPA6NGQ23I2D: score=1 
    TLE6Q9H8083I2D: score=1 
    About this table

    Gene Ontology (GO): 3 biological process terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0006468protein phosphorylation IEA--
    GO:0007094mitotic cell cycle spindle assembly checkpoint IEA--
    GO:0090307spindle assembly involved in mitosis IEA--


    KHDC3L for ontologies           About GeneDecksing



    Drugs & Compounds
    for KHDC3L gene

    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
    About This Section
    Browse Small Molecules at EMD Millipore
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    Browse Tocris compounds for KHDC3L
    Search CenterWatch for drugs/clinical trials and news about KHDC3L / KHD3L 

    Transcripts
    for KHDC3L gene

    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 235 Homo sapiens; Mar 10 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    RNAi Products from EMD Millipore,
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    About This Section
    REFSEQ mRNAs for KHDC3L gene: 
    NM_001017361.2  

    Unigene Cluster for KHDC3L:

    KH domain containing 3-like, subcortical maternal complex member
    Hs.128326  [show with all ESTs]
    Unigene Representative Sequence: AB211062
    1 Ensembl transcript including schematic representation, and UCSC links where relevant:
    ENST00000370367(uc003pgt.4)

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    Inhib. RNA
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    Additional cDNA sequence: 

    AB211062.1 BC132844.1 BC137160.1 

    1 DOTS entry:

    DT.205070 

    14 AceView cDNA sequences:

    AA872619 AI652239 BE550370 AA580965 AA973759 AI955057 AI917825 AI655845 
    AA581033 AI651751 AI631547 AW136207 AI638315 AI371978 

    GeneLoc Exon Structure


    Expression
    for KHDC3L gene

    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
    About This Section
    		 See probesets specificity/sensitivity at GeneAnnot
    CGAP TAG: --


    KHDC3L expression in embryonic tissues and stem cells
    Expression by the Database of Embryonic development, Stem cell research, and Regenerative medicine    About this table
    1 LifeMap In Vivo Development Anatomical Compartment/Cell 
    Tissue Anatomical Compartment CellCategory (developmental path)
    OvaryAntral FollicleSecondary OocyteFemale Gametocytes, Germ Cells
    Expression: Positive    Negative     Selective marker
    Experimental details: Curated     Microarrays     In-situ hybridization
    Stem Cell Differentiation: 1 LifeMap Cell 
    NameCategory
    Sox17-GFP genetically modified stem cells (Embryonic Stem Cell)Early Embryo, Inner Cell Mass

    See KHDC3L Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for KHDC3L

    SOURCE GeneReport for Unigene cluster: Hs.128326

    UniProtKB/Swiss-Prot: KHD3L_HUMAN, Q587J8
    Tissue specificity: Expression appears to be maximal in germinal vesicle oocytes, it tails off through metaphase II
    oocytes and is undetectable following the completion of the oocyte to embryo transition

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    In Situ
    Assay Products:     
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    Orthologs
    for KHDC3L gene

    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
    About This Section
    		   --

    ENSEMBL Gene Tree for KHDC3L (if available)
    TreeFam Gene Tree for KHDC3L (if available) 

    Paralogs
    for KHDC3L gene

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for KHDC3L gene
    OOEP2  
    2 SIMAP similar genes for KHDC3L using alignment to 1 protein entry:     KHD3L_HUMAN:
    DPPA5    OOEP

    KHDC3L for paralogs           About GeneDecksing


    1 Pseudogenes.org Pseudogene for KHDC3L
    PGOHUM00000246124


    Genomic Variants
    for KHDC3L gene

    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
    About This Section

    10/79 NCBI SNPs in KHDC3L are shown (see all 79)     About this table
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance    		Chr 6 posSequence#AA
    Chg    		TypeMore#Allele
    freq    		PopTotal
    sample    		More
    ----------
    rs1180626821,2
    		C,F,--71268897(+) TGTGAC/TTGGTG 1 -- us2k11Minor allele frequency- T:0.04NA 120
    rs1132931871,2
    		C--71269133(+) AGTTCG/AAGCGA 1 -- us2k11Minor allele frequency- A:0.00CSA 1
    rs1132721771,2
    		C,--71270248(+) GCCAAC/TCTGGG 1 -- us2k11Minor allele frequency- T:0.50NA 2
    rs802271381,2
    		F,--71270445(+) GGAAAC/TGTAGT 1 -- us2k11Minor allele frequency- T:0.08EA 120
    rs1163703481,2
    		C,F,--71270572(+) CTCCCG/ACTGGG 1 -- us2k11Minor allele frequency- A:0.03WA 118
    rs802035761,2
    		F,--71270816(+) ACCGCG/AGTTCT 1 -- us2k11Minor allele frequency- A:0.03WA 118
    rs753476181,2
    		C,--71270910(+) GGCGGG/TTTCCG 2 V F mis10--------
    rs117574331,2
    		C,H--71270982(+) AGCGGT/GTCTCC 2 /V /F mis1 ese35Minor allele frequency- G:0.00NS EA NA 396
    rs617466891,2
    		F--71271908(+) ACCCAG/TCAGTC 2 Q H mis11Minor allele frequency- T:0.14NS 52
    rs617406171,2
    		F--71272008(+) ACCCAG/TTTACT 2 V F mis11Minor allele frequency- T:0.16NS 44

    HapMap Linkage Disequilibrium report for KHDC3L (74072400 - 74073898 bp)
    Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
          Database of Genomic Variants (DGV) variations for KHDC3L: --

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    Disorders / Diseases
    for KHDC3L gene

    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
    About This Section
    KHDC3L for disorders           About GeneDecksing

    OMIM gene information: 611687    OMIM disorders: --

    UniProtKB/Swiss-Prot: KHD3L_HUMAN, Q587J8
  • Defects in KHDC3L are the cause of hydatidiform mole recurrent type 2 (HYDM2) [MIM:614293]. A disorder
    • characterized by excessive trophoblast development that produces a growing mass of tissue inside the uterus at the
    beginning of a pregnancy. It leads to abnormal pregnancies with no embryo, and cystic degeneration of the chorionic
    villi

    1 disease for KHDC3L:    About MalaCards
    hydatidiform mole, recurrent


    Export disorders for KHDC3L gene to outside databases

    Publications
    for KHDC3L gene

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
    About This Section

    PubMed articles for KHDC3L gene integrated from 9 sources:
    (articles sorted by number of sources associating them with KHDC3L)    		    Utopia: connect your pdf to the dynamic
    world of online information

    1. Mutations causing familial biparental hydatidiform mole implicate c6orf221 as a possible regulator of genomic imprinting in the human oocyte. (PubMed id 21885028)1, 2, 3 Parry D.A.... Sheridan E.G. (2011)
    2. Atypical structure and phylogenomic evolution of the new eutherian oocyte-and embryo-expressed KHDC1/DPPA5/ECAT1/OOEP gene family. (PubMed id 17913455)1, 2 Pierre A.... Monget P. (2007)
    3. The homeoprotein Nanog is required for maintenance of pluripotency in mouse epiblast and ES cells. (PubMed id 12787504)1, 2 Mitsui K.... Yamanaka S. (2003)
    4. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)2 Gerhard D.S....Malek J. (2004)
    5. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)1 Strausberg R.L....Marra M.A. (2002)

    External Searches for KHDC3L gene

    (in PubMed, OMIM, and NCBI Bookshelf)
    About This Section
     ANDOR
    Aliases
    Free Text  
      Query String
    		PubMed
    OMIM
    NCBI Bookshelf
      (Note: In FireFox, select the above section and copy using Ctrl-C)

    Genome Databases showing KHDC3L gene

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
    About This Section
    Entrez Gene: 154288 HGNC: 33699 AceView: LOC154288 Ensembl:ENSG00000203908 euGenes: HUgn154288
    ECgene: KHDC3L H-InvDB: KHDC3L

    Other Databases showing KHDC3L gene

    (According to HUGE)
    About This Section
    		   --

    Specialized Databases showing KHDC3L gene

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
    Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
    About This Section
    NameDescription
    PharmGKB entry for KHDC3L Pharmacogenomics, SNPs, Pathways

    Intellectual Property
    for KHDC3L gene

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
    About This Section
    		Patent Information for KHDC3L gene:
    Search GeneIP for patents involving KHDC3L

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



    Products
    for KHDC3L gene

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    About This Section

     
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    GeneCards Homepage - Last full update: 18 Mar 2013 - Incrementals: 21 Mar 2013 , 15 Apr 2013 , 26 Apr 2013

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    von Willebrand factor
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