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Aliases for MCPH1 Gene

Aliases for MCPH1 Gene

  • Microcephalin 1 2 3 5
  • BRCT-Repeat Inhibitor Of TERT Expression 1 2 3
  • Microcephaly, Primary Autosomal Recessive 1 2
  • BRIT1 3
  • MCT 3

External Ids for MCPH1 Gene

Previous GeneCards Identifiers for MCPH1 Gene

  • GC08U990048
  • GC08P006276
  • GC08P006046

Summaries for MCPH1 Gene

Entrez Gene Summary for MCPH1 Gene

  • This gene encodes a DNA damage response protein. The encoded protein may play a role in G2/M checkpoint arrest via maintenance of inhibitory phosphorylation of cyclin-dependent kinase 1. Mutations in this gene have been associated with primary autosomal recessive microcephaly 1 and premature chromosome condensation syndrome. Alternatively spliced transcript variants have been described. [provided by RefSeq, Feb 2010]

GeneCards Summary for MCPH1 Gene

MCPH1 (Microcephalin 1) is a Protein Coding gene. Diseases associated with MCPH1 include Microcephaly 1, Primary, Autosomal Recessive and Autosomal Recessive Primary Microcephaly. Among its related pathways are Cell Cycle, Mitotic and DNA Damage. GO annotations related to this gene include identical protein binding.

UniProtKB/Swiss-Prot for MCPH1 Gene

  • Implicated in chromosome condensation and DNA damage induced cellular responses. May play a role in neurogenesis and regulation of the size of the cerebral cortex.

No data available for Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for MCPH1 Gene

Genomics for MCPH1 Gene

Regulatory Elements for MCPH1 Gene

Enhancers for MCPH1 Gene
GeneHancer Identifier Score Enhancer Sources TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Other Gene Targets for Enhancer

Enhancers around MCPH1 on UCSC Golden Path with GeneCards custom track

Promoters for MCPH1 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters

ENSRs around MCPH1 on UCSC Golden Path with GeneCards custom track

Genomic Location for MCPH1 Gene

6,406,592 bp from pter
6,648,504 bp from pter
241,913 bases
Plus strand

Genomic View for MCPH1 Gene

Genes around MCPH1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
MCPH1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for MCPH1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for MCPH1 Gene

Proteins for MCPH1 Gene

  • Protein details for MCPH1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Protein Accession:
    Secondary Accessions:
    • B4DWW2
    • E9PGU5
    • E9PH63
    • Q66GU1
    • Q9H9C7

    Protein attributes for MCPH1 Gene

    835 amino acids
    Molecular mass:
    92877 Da
    Quaternary structure:
    • Interacts with CDC27 and maybe other components of the APC/C complex. Interacts with histone variant H2AFX under DNA damage conditions.
    • MCPH1 deficient cells exhibit a delay in post-mitotic chromosome decondensation.

    Three dimensional structures from OCA and Proteopedia for MCPH1 Gene

    Alternative splice isoforms for MCPH1 Gene


neXtProt entry for MCPH1 Gene

Proteomics data for MCPH1 Gene at MOPED

Post-translational modifications for MCPH1 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for MCPH1 Gene

No data available for DME Specific Peptides for MCPH1 Gene

Domains & Families for MCPH1 Gene

Protein Domains for MCPH1 Gene

Suggested Antigen Peptide Sequences for MCPH1 Gene

Graphical View of Domain Structure for InterPro Entry



  • BRCT domain 1 is required to prevent abnormal chromosome condensation. It binds directly to the SWI-SNF chromatin remodeling complex (PubMed:19925808).
  • BRCT domain 1 is required to prevent abnormal chromosome condensation. It binds directly to the SWI-SNF chromatin remodeling complex (PubMed:19925808).
  • BRCT domains 2 and 3 recognize phosphoserine/phosphothreonine marks on proteins with high selectivity, and mediate interaction with phosphorylated CDC27. They also mediate the dual recognition of phosphoserine and phosphotyrosine in the C-terminal tail of histone H2AFX (PubMed:22139841, PubMed:22908299 and PubMed:22908299).
  • Contains 3 BRCT domains.
genes like me logo Genes that share domains with MCPH1: view

No data available for Gene Families for MCPH1 Gene

Function for MCPH1 Gene

Molecular function for MCPH1 Gene

UniProtKB/Swiss-Prot Function:
Implicated in chromosome condensation and DNA damage induced cellular responses. May play a role in neurogenesis and regulation of the size of the cerebral cortex.
genes like me logo Genes that share phenotypes with MCPH1: view

Human Phenotype Ontology for MCPH1 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for MCPH1 Gene

MGI Knock Outs for MCPH1:

Animal Model Products

miRNA for MCPH1 Gene

miRTarBase miRNAs that target MCPH1

No data available for Enzyme Numbers (IUBMB) , Gene Ontology (GO) - Molecular Function , Transcription Factor Targets and HOMER Transcription for MCPH1 Gene

Localization for MCPH1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for MCPH1 Gene

Cytoplasm, cytoskeleton, microtubule organizing center, centrosome.

Subcellular locations from

Jensen Localization Image for MCPH1 Gene COMPARTMENTS Subcellular localization image for MCPH1 gene
Compartment Confidence
nucleus 5
cytoskeleton 4
cytosol 3

No data available for Gene Ontology (GO) - Cellular Components for MCPH1 Gene

Pathways & Interactions for MCPH1 Gene

genes like me logo Genes that share pathways with MCPH1: view

Pathways by source for MCPH1 Gene

1 Cell Signaling Technology pathway for MCPH1 Gene

Gene Ontology (GO) - Biological Process for MCPH1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000278 mitotic cell cycle TAS --
GO:0010468 regulation of gene expression IEA --
GO:0046605 regulation of centrosome cycle IEA --
GO:0060348 bone development IEA --
GO:0060623 regulation of chromosome condensation IEA --
genes like me logo Genes that share ontologies with MCPH1: view

No data available for SIGNOR curated interactions for MCPH1 Gene

Drugs & Compounds for MCPH1 Gene

No Compound Related Data Available

Transcripts for MCPH1 Gene

Unigene Clusters for MCPH1 Gene

Microcephalin 1:
Representative Sequences:

Alternative Splicing Database (ASD) splice patterns (SP) for MCPH1 Gene

No ASD Table

Relevant External Links for MCPH1 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for MCPH1 Gene

mRNA expression in normal human tissues for MCPH1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for MCPH1 Gene

This gene is overexpressed in CD8 Tcells (42.2) and Fetal gut (26.5).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MOPED, and MaxQB for MCPH1 Gene

SOURCE GeneReport for Unigene cluster for MCPH1 Gene Hs.656769

mRNA Expression by UniProt/SwissProt for MCPH1 Gene

Tissue specificity: Expressed in fetal brain, liver and kidney.
genes like me logo Genes that share expression patterns with MCPH1: view

Protein tissue co-expression partners for MCPH1 Gene

- Elite partner

Primer Products

No data available for mRNA differential expression in normal tissues for MCPH1 Gene

Orthologs for MCPH1 Gene

This gene was present in the common ancestor of animals.

Orthologs for MCPH1 Gene

Organism Taxonomy Gene Similarity Type Details
(Bos Taurus)
Mammalia MCPH1 35
  • 67.91 (n)
  • 58.62 (a)
MCPH1 36
  • 57 (a)
(Canis familiaris)
Mammalia MCPH1 35
  • 75.03 (n)
  • 63.85 (a)
MCPH1 36
  • 57 (a)
(Mus musculus)
Mammalia Mcph1 35
  • 71.45 (n)
  • 59.55 (a)
Mcph1 16
Mcph1 36
  • 57 (a)
(Pan troglodytes)
Mammalia MCPH1 35
  • 98.96 (n)
  • 98.2 (a)
MCPH1 36
  • 98 (a)
(Rattus norvegicus)
Mammalia Mcph1 35
  • 71.6 (n)
  • 58.7 (a)
(Monodelphis domestica)
Mammalia -- 36
  • 27 (a)
-- 36
  • 72 (a)
-- 36
  • 63 (a)
(Ornithorhynchus anatinus)
Mammalia -- 36
  • 36 (a)
-- 36
  • 52 (a)
(Gallus gallus)
Aves MCPH1 35
  • 65.13 (n)
  • 59.3 (a)
MCPH1 36
  • 45 (a)
(Anolis carolinensis)
Reptilia MCPH1 36
  • 58 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia Str.17324 35
(Danio rerio)
Actinopterygii Dr.15463 35
mcph1 36
  • 46 (a)
fruit fly
(Drosophila melanogaster)
Insecta MCPH1 36
  • 16 (a)
sea squirt
(Ciona savignyi)
Ascidiacea CSA.10623 36
  • 23 (a)
Species with no ortholog for MCPH1:
  • 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)
  • 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)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • 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)
  • worm (Caenorhabditis elegans)

Evolution for MCPH1 Gene

Gene Tree for MCPH1 (if available)
Gene Tree for MCPH1 (if available)

Paralogs for MCPH1 Gene

No data available for Paralogs for MCPH1 Gene

Variants for MCPH1 Gene

Sequence variations from dbSNP and Humsavar for MCPH1 Gene

SNP ID Clin Chr 08 pos Sequence Context AA Info Type
VAR_046745 Microcephaly 1, primary, autosomal recessive (MCPH1)
rs2442513 - 6,439,029(-) TGGTG(A/C/G)CTACT intron-variant, reference, missense, utr-variant-5-prime
rs2922828 - 6,442,120(-) AGGTG(C/T)TTCAC reference, missense
rs34121009 - 6,444,512(+) TGTGT(A/G)TTTCT reference, missense
rs35590577 - 6,444,585(+) AAGTC(A/C)TCAGA reference, missense

Structural Variations from Database of Genomic Variants (DGV) for MCPH1 Gene

Variant ID Type Subtype PubMed ID
nsv890034 CNV Gain 21882294
nsv890041 CNV Gain 21882294
nsv527005 CNV Gain 19592680
nsv890055 CNV Gain 21882294
nsv524404 CNV Loss 19592680
esv2736530 CNV Deletion 23290073
esv2736531 CNV Deletion 23290073
dgv443n21 CNV Loss 19592680
esv2668625 CNV Deletion 23128226
dgv444n21 CNV Loss 19592680
nsv6057 CNV Insertion 18451855
nsv890056 CNV Loss 21882294
nsv890057 CNV Gain 21882294
nsv890058 CNV Gain 21882294
esv1010135 CNV Insertion 20482838
esv2422383 CNV Duplication 17116639
esv2736532 CNV Deletion 23290073
nsv397733 CNV Loss 16902084
nsv522043 CNV Loss 19592680
esv2736533 CNV Deletion 23290073
esv2736534 CNV Deletion 23290073
nsv6058 CNV Insertion 18451855
nsv526417 CNV Loss 19592680
nsv521585 CNV Loss 19592680
nsv890059 CNV Loss 21882294
nsv524670 CNV Loss 19592680

Variation tolerance for MCPH1 Gene

Residual Variation Intolerance Score: 99.2% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 14.20; 96.20% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for MCPH1 Gene

Human Gene Mutation Database (HGMD)

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for MCPH1 Gene

Disorders for MCPH1 Gene

MalaCards: The human disease database

(10) MalaCards diseases for MCPH1 Gene - From: OMIM, ClinVar, GeneTests, Orphanet, Swiss-Prot, DISEASES, Novoseek, and GeneCards

- elite association - COSMIC cancer census association via MalaCards
Search MCPH1 in MalaCards View complete list of genes associated with diseases


  • Microcephaly 1, primary, autosomal recessive (MCPH1) [MIM:251200]: A disease defined as a head circumference more than 3 standard deviations below the age-related mean. Brain weight is markedly reduced and the cerebral cortex is disproportionately small. Despite this marked reduction in size, the gyral pattern is relatively well preserved, with no major abnormality in cortical architecture. Affected individuals are mentally retarded. Primary microcephaly is further defined by the absence of other syndromic features or significant neurological deficits due to degenerative brain disorder. Some MCHP1 patients also present growth retardation, short stature, and misregulated chromosome condensation as indicated by a high number of prophase-like cells detected in routine cytogenetic preparations and poor-quality metaphase G-banding. {ECO:0000269 PubMed:12046007, ECO:0000269 PubMed:15199523, ECO:0000269 PubMed:16211557}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Relevant External Links for MCPH1

Genetic Association Database (GAD)
Human Genome Epidemiology (HuGE) Navigator
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
genes like me logo Genes that share disorders with MCPH1: view

No data available for Genatlas for MCPH1 Gene

Publications for MCPH1 Gene

  1. A common SNP of MCPH1 is associated with cranial volume variation in Chinese population. (PMID: 18204051) Wang J.-K. … Su B. (Hum. Mol. Genet. 2008) 3 4 48 67
  2. MCPH1 functions in an H2AX-dependent but MDC1-independent pathway in response to DNA damage. (PMID: 17925396) Wood J.L. … Chen J. (J. Biol. Chem. 2007) 2 3 23
  3. Sex-dependent association of common variants of microcephaly genes with brain structure. (PMID: 20080800) Rimol L.M. … Andreassen O.A. (Proc. Natl. Acad. Sci. U.S.A. 2010) 3 23
  4. BRIT1/MCPH1 is essential for mitotic and meiotic recombination DNA repair and maintaining genomic stability in mice. (PMID: 20107607) Liang Y. … Li K. (PLoS Genet. 2010) 3 23
  5. The c.940G variant of the Microcephalin (MCPH1) gene is not associated with microcephaly or mental retardation. (PMID: 19267414) Maghirang-Rodriguez R. … Collins J.S. (Am. J. Med. Genet. A 2009) 3 23

Products for MCPH1 Gene

Sources for MCPH1 Gene