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Aliases for KHDC3L Gene

Aliases for KHDC3L Gene

  • KH Domain Containing 3 Like, Subcortical Maternal Complex Member 2 3 5
  • ES Cell-Associated Transcript 1 Protein 3 4
  • C6orf221 3 4
  • ECAT1 3 4
  • KH Domain Containing 3-Like, Subcortical Maternal Complex Member 2
  • Chromosome 6 Open Reading Frame 221 2
  • ES Cell Associated Transcript 1 2
  • KHDC3-Like Protein 3
  • HYDM2 3

External Ids for KHDC3L Gene

Previous HGNC Symbols for KHDC3L Gene

  • C6orf221

Previous GeneCards Identifiers for KHDC3L Gene

  • GC06P074073

Summaries for KHDC3L Gene

Entrez Gene Summary for KHDC3L Gene

  • 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]

GeneCards Summary for KHDC3L Gene

KHDC3L (KH Domain Containing 3 Like, Subcortical Maternal Complex Member) is a Protein Coding gene. Diseases associated with KHDC3L include Hydatidiform Mole, Recurrent, 2 and Hydatidiform Mole, Recurrent, 1. Gene Ontology (GO) annotations related to this gene include RNA binding. An important paralog of this gene is OOEP.

Additional gene information for KHDC3L Gene

No data available for CIViC summary , UniProtKB/Swiss-Prot , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for KHDC3L Gene

Genomics for KHDC3L Gene

GeneHancer (GH) Regulatory Elements for KHDC3L Gene

Promoters and enhancers for KHDC3L 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
GH06I073362 Promoter 0.5 EPDnew 550.8 +0.4 428 0.1 KHDC3L OOEP-AS1
GH06I073262 Promoter/Enhancer 1.8 EPDnew Ensembl ENCODE 10 -98.5 -98477 3.4 PKNOX1 RB1 SIN3A ZBTB40 ZNF335 ZNF121 GLIS2 ETV6 SMARCA5 CBFB ENSG00000229852 ENSG00000243501 KHDC1 EIF3EP1 MTO1 DPPA5 KHDC3L RPSAP41
GH06I073388 Enhancer 1.2 Ensembl ENCODE 11.5 +26.8 26798 1.3 ATF1 ARNT ZNF2 POLR2B ZNF766 GLIS2 ZNF143 KLF7 ATF7 GTF2B EEF1A1 KHDC3L DPPA5 RPS6P8 OOEP RPL39P3
GH06I073326 Enhancer 0.6 ENCODE 11.1 -35.4 -35418 0.2 CTCF ZNF654 ARNT TRIM22 REST RAD21 MAFF SKIL KLF16 ZNF143 PAICSP3 DPPA5 KHDC3L SDCBP2P1
GH06I073234 Enhancer 0.6 ENCODE 10.7 -126.5 -126537 2.4 ZNF146 JUN MAX CEBPB EP300 ZBTB40 SP1 JUND MAFF STAT3 GC06P073237 ENSG00000243501 ENSG00000229852 KHDC1 KHDC3L DPPA5 KHDC1L
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around KHDC3L on UCSC Golden Path with GeneCards custom track

Genomic Locations for KHDC3L Gene

Genomic Locations for KHDC3L Gene
1,965 bases
Plus strand

Genomic View for KHDC3L Gene

Genes around KHDC3L on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
KHDC3L Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for KHDC3L Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for KHDC3L Gene

Proteins for KHDC3L Gene

  • Protein details for KHDC3L Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    KHDC3-like protein
    Protein Accession:
    Secondary Accessions:
    • B2RNW7

    Protein attributes for KHDC3L Gene

    217 amino acids
    Molecular mass:
    24306 Da
    Quaternary structure:
    • Component of the subcortical maternal complex (SCMC) which is essential for progression of zygotes beyond the first embryonic cell division. The complex also contains NLRP5, OOEP and TLE6.

neXtProt entry for KHDC3L Gene

Post-translational modifications for KHDC3L Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for KHDC3L Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for KHDC3L Gene

Domains & Families for KHDC3L Gene

Gene Families for KHDC3L Gene

Human Protein Atlas (HPA):
  • Disease related genes
  • Predicted intracellular proteins

Protein Domains for KHDC3L Gene

Suggested Antigen Peptide Sequences for KHDC3L Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry



  • Contains an atypical KH domain with amino acid changes at critical sites, suggesting that it may not bind RNA.
  • Belongs to the KHDC1 family.
  • Contains an atypical KH domain with amino acid changes at critical sites, suggesting that it may not bind RNA.
  • Belongs to the KHDC1 family.
genes like me logo Genes that share domains with KHDC3L: view

Function for KHDC3L Gene

Gene Ontology (GO) - Molecular Function for KHDC3L Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003723 RNA binding IEA --
GO:0005515 protein binding IPI 26537248
genes like me logo Genes that share ontologies with KHDC3L: view
genes like me logo Genes that share phenotypes with KHDC3L: view

Human Phenotype Ontology for KHDC3L Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for KHDC3L Gene

MGI Knock Outs for KHDC3L:

Animal Model Products

CRISPR Products

miRNA for KHDC3L Gene

miRTarBase miRNAs that target KHDC3L

Inhibitory RNA Products

No data available for Molecular function , Enzyme Numbers (IUBMB) , Phenotypes From GWAS Catalog , Transcription Factor Targets and HOMER Transcription for KHDC3L Gene

Localization for KHDC3L Gene

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 KHDC3L gene
Compartment Confidence
mitochondrion 3
nucleus 1
cytosol 1

Gene Ontology (GO) - Cellular Components for KHDC3L Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0043234 protein complex IDA 26537248
genes like me logo Genes that share ontologies with KHDC3L: view

No data available for Subcellular locations from UniProtKB/Swiss-Prot and Subcellular locations from the Human Protein Atlas (HPA) for KHDC3L Gene

Pathways & Interactions for KHDC3L Gene

SuperPathways for KHDC3L Gene

No Data Available

Gene Ontology (GO) - Biological Process for KHDC3L Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0008150 biological_process ND --
genes like me logo Genes that share ontologies with KHDC3L: view

No data available for Pathways by source and SIGNOR curated interactions for KHDC3L Gene

Drugs & Compounds for KHDC3L Gene

No Compound Related Data Available

Transcripts for KHDC3L Gene

mRNA/cDNA for KHDC3L Gene

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

Unigene Clusters for KHDC3L Gene

KH domain containing 3-like, subcortical maternal complex member:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Alternative Splicing Database (ASD) splice patterns (SP) for KHDC3L Gene

No ASD Table

Relevant External Links for KHDC3L Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for KHDC3L Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for KHDC3L Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for KHDC3L Gene

This gene is overexpressed in Brain - Cerebellar Hemisphere (x8.5), Brain - Cerebellum (x7.5), Brain - Hippocampus (x4.3), Brain - Putamen (basal ganglia) (x4.3), and Brain - Nucleus accumbens (basal ganglia) (x4.2).

NURSA nuclear receptor signaling pathways regulating expression of KHDC3L Gene:


SOURCE GeneReport for Unigene cluster for KHDC3L Gene:


mRNA Expression by UniProt/SwissProt for KHDC3L Gene:

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.

Phenotype-based relationships between genes and organs from Gene ORGANizer for KHDC3L Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
  • endocrine
  • reproductive
  • urinary
genes like me logo Genes that share expression patterns with KHDC3L: view

No data available for Protein differential expression in normal tissues , Protein expression , Protein tissue co-expression partners and Evidence on tissue expression from TISSUES for KHDC3L Gene

Orthologs for KHDC3L Gene

This gene was present in the common ancestor of mammals.

Orthologs for KHDC3L Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia KHDC3L 33
  • 99.08 (n)
C6H6ORF221 34
  • 99 (a)
(Bos Taurus)
Mammalia KHDC3L 33 34
  • 74.11 (n)
(Canis familiaris)
Mammalia LOC481879 33
  • 72.03 (n)
  • 28 (a)
(Rattus norvegicus)
Mammalia Khdc3 33
  • 59.65 (n)
(Mus musculus)
Mammalia Khdc3 33 16 34
  • 58.96 (n)
Gm20509 34
  • 22 (a)
Species where no ortholog for KHDC3L 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)
  • chicken (Gallus gallus)
  • 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)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • lizard (Anolis carolinensis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • oppossum (Monodelphis domestica)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • platypus (Ornithorhynchus anatinus)
  • rainbow trout (Oncorhynchus mykiss)
  • 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)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)
  • zebrafish (Danio rerio)

Evolution for KHDC3L Gene

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

Paralogs for KHDC3L Gene

Paralogs for KHDC3L Gene

(2) SIMAP similar genes for KHDC3L Gene using alignment to 1 proteins: Pseudogenes for KHDC3L Gene

genes like me logo Genes that share paralogs with KHDC3L: view

Variants for KHDC3L Gene

Sequence variations from dbSNP and Humsavar for KHDC3L Gene

SNP ID Clin Chr 06 pos Variation AA Info Type
rs606231233 pathogenic, Hydatidiform mole, recurrent, 2 73,362,732(+) G/T initiator_codon_variant, missense_variant
rs606231234 pathogenic, Hydatidiform mole, recurrent, 2 73,363,245(+) CTGACT/CT coding_sequence_variant, frameshift
rs606231235 pathogenic, Hydatidiform mole, recurrent, 2 73,362,730(+) A/G initiator_codon_variant, missense_variant
rs606231286 pathogenic, Hydatidiform mole, recurrent, 2 73,363,221(+) CAATCAA/CAA coding_sequence_variant, frameshift
rs745776920 likely-pathogenic, Hydatidiform mole, recurrent, 2 73,363,259(+) C/T coding_sequence_variant, stop_gained

Structural Variations from Database of Genomic Variants (DGV) for KHDC3L Gene

Variant ID Type Subtype PubMed ID
esv2732291 CNV deletion 23290073
esv2732292 CNV deletion 23290073
nsv830693 CNV loss 17160897

Variation tolerance for KHDC3L Gene

Residual Variation Intolerance Score: 61.1% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 4.67; 65.85% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for KHDC3L Gene

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

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for KHDC3L Gene

Disorders for KHDC3L Gene

MalaCards: The human disease database

(8) MalaCards diseases for KHDC3L Gene - From: HGMD, OMIM, ClinVar, GTR, Orphanet, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
hydatidiform mole, recurrent, 2
  • hydatidiform mole, complete
hydatidiform mole, recurrent, 1
  • hydm1
partial hydatidiform mole
  • incomplete hydatidiform mole
gestational trophoblastic neoplasm
  • hydatidiform mole, recurrent, 1
  • chromosome triploidy syndrome
- elite association - COSMIC cancer census association via MalaCards


  • Hydatidiform mole, recurrent, 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. {ECO:0000269 PubMed:21885028}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Additional Disease Information for KHDC3L

genes like me logo Genes that share disorders with KHDC3L: view

No data available for Genatlas for KHDC3L Gene

Publications for KHDC3L Gene

  1. Mutations causing familial biparental hydatidiform mole implicate c6orf221 as a possible regulator of genomic imprinting in the human oocyte. (PMID: 21885028) Parry DA … Sheridan EG (American journal of human genetics 2011) 2 3 4 58
  2. TLE6 mutation causes the earliest known human embryonic lethality. (PMID: 26537248) Alazami AM … Alkuraya FS (Genome biology 2015) 3 4 58
  3. Atypical structure and phylogenomic evolution of the new eutherian oocyte- and embryo-expressed KHDC1/DPPA5/ECAT1/OOEP gene family. (PMID: 17913455) Pierre A … Monget P (Genomics 2007) 3 4 58
  4. The homeoprotein Nanog is required for maintenance of pluripotency in mouse epiblast and ES cells. (PMID: 12787504) Mitsui K … Yamanaka S (Cell 2003) 3 4 58
  5. No evidence for mutations in NLRP7, NLRP2 or KHDC3L in women with unexplained recurrent pregnancy loss or infertility. (PMID: 25376457) Aghajanova L … Van den Veyver IB (Human reproduction (Oxford, England) 2015) 3 58

Products for KHDC3L Gene

Sources for KHDC3L Gene

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