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Aliases for KHDC3L Gene

Aliases for KHDC3L Gene

  • KH Domain Containing 3-Like, Subcortical Maternal Complex Member 2 3
  • ES Cell-Associated Transcript 1 Protein 3 4
  • C6orf221 3 4
  • ECAT1 3 4
  • Chromosome 6 Open Reading Frame 221 2
  • ES Cell Associated Transcript 1 2
  • 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. GO annotations related to this gene include RNA binding. An important paralog of this gene is OOEP.

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

Genomics for KHDC3L Gene

Genomic Location for KHDC3L Gene

73,362,211 bp from pter
73,364,175 bp from pter
1,965 bases
Plus strand

Genomic View for KHDC3L Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for KHDC3L Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for KHDC3L Gene

No data available for Regulatory Elements 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:
    No Data Available

neXtProt entry for KHDC3L Gene

Proteomics data for KHDC3L Gene at MOPED

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

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
  • Contains 1 KH domain.
  • Belongs to the KHDC1 family.
genes like me logo Genes that share domains with KHDC3L: view

No data available for Gene Families for KHDC3L Gene

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 --
genes like me logo Genes that share ontologies with KHDC3L: view
genes like me logo Genes that share phenotypes with KHDC3L: view

Animal Models for KHDC3L Gene

MGI Knock Outs for KHDC3L:

Animal Model Products

CRISPR Products

miRNA for KHDC3L Gene

miRTarBase miRNAs that target KHDC3L

miRNA Products

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for KHDC3L

In Situ Assay Products

Flow Cytometry Products

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

Localization for KHDC3L Gene

No data available for Subcellular locations from UniProtKB/Swiss-Prot , Subcellular locations from COMPARTMENTS and Gene Ontology (GO) - Cellular Components for KHDC3L Gene

Pathways & Interactions for KHDC3L Gene

SuperPathways for KHDC3L Gene

No Data Available

Gene Ontology (GO) - Biological Process for KHDC3L Gene


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

(2) 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

miRNA Products

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for KHDC3L

Flow Cytometry 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 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).

SOURCE GeneReport for Unigene cluster for KHDC3L Gene Hs.128326

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.
genes like me logo Genes that share expression patterns with KHDC3L: view

Primer Products

  • QuantiTect SYBR Green Assays in human,mouse,rat
  • Pre-validated RT² qPCR Primer Assay in human,mouse,rat
  • QuantiFast Probe-based Assays in human,mouse,rat

In Situ Assay Products

No data available for Protein differential expression in normal tissues , Protein expression and Protein tissue co-expression partners 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
(Bos Taurus)
Mammalia KHDC3L 35
  • 74.11 (n)
  • 62.33 (a)
  • 48 (a)
(Canis familiaris)
Mammalia LOC481879 35
  • 72.03 (n)
  • 60.8 (a)
  • 28 (a)
(Mus musculus)
Mammalia Khdc3 35
  • 58.96 (n)
  • 42.92 (a)
Khdc3 16
Gm20509 36
  • 22 (a)
Khdc3 36
  • 17 (a)
(Pan troglodytes)
Mammalia KHDC3L 35
  • 99.08 (n)
  • 98.62 (a)
C6H6ORF221 36
  • 99 (a)
(Rattus norvegicus)
Mammalia Khdc3 35
  • 59.65 (n)
  • 41.15 (a)
Species with no ortholog for KHDC3L:
  • 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 Sequence Context AA Info Type MAF
rs508770 -- 73,360,969(+) GAGTT(C/T)AAGCG upstream-variant-2KB
rs550423 -- 73,360,971(-) ATCGC(C/T)TGAAC upstream-variant-2KB
rs561930 - 73,363,808(+) CAAGG(C/G/T)AGTGA reference, missense, downstream-variant-500B
rs564533 - 73,363,214(-) GTCCT(C/G)CTGGT missense, reference
rs1713860 -- 73,360,494(-) actta(A/G)agggt upstream-variant-2KB

Variation tolerance for KHDC3L Gene

Residual Variation Intolerance Score: 61.11% 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)

Relevant External Links for KHDC3L Gene

HapMap Linkage Disequilibrium report
Human Gene Mutation Database (HGMD)

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Structural Variations from Database of Genomic Variants (DGV) for KHDC3L Gene

Disorders for KHDC3L Gene

MalaCards: The human disease database

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

Disorder Aliases PubMed IDs
hydatidiform mole, recurrent, 2
  • hydatidiform mole complete
hydatidiform mole, recurrent, 1
  • gestational trophoblastic disease
partial hydatidiform mole
  • incomplete hydatidiform mole
gestational trophoblastic neoplasm
  • hydatidiform mole, recurrent, 1
  • chromosome triploidy syndrome
- elite association


  • 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.

Relevant External Links for KHDC3L

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
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 D.A. … Sheridan E.G. (Am. J. Hum. Genet. 2011) 2 67
  2. Absence of KHDC3L mutations in Chinese patients with recurrent and sporadic hydatidiform moles. (PMID: 24215781) Zhao W. … Qian J. (Cancer Genet 2013) 67
  3. No evidence for mutations in NLRP7 and KHDC3L in women with androgenetic hydatidiform moles. (PMID: 24105752) Mahadevan S. … Van den Veyver I.B. (Prenat. Diagn. 2013) 67
  4. Maternal NLRP7 and C6orf221 variants are not a common risk factor for androgenetic moles, triploidy and recurrent miscarriage. (PMID: 23515668) Manokhina I. … Robinson W.P. (Mol. Hum. Reprod. 2013) 67
  5. NLRP7 or KHDC3L genes and the etiology of molar pregnancies and recurrent miscarriage. (PMID: 23963444) Andreasen L. … Sunde L. (Mol. Hum. Reprod. 2013) 67

Products for KHDC3L Gene

Sources for KHDC3L Gene

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