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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
  • Truncated Microcephalin 3
  • Microcephalin 3
  • 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 Primary Microcephaly. Among its related pathways are DNA Damage and Cell Cycle, Mitotic. 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.

Additional gene information for MCPH1 Gene

No data available for CIViC summary , 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 Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH08H006647 1.3 Ensembl ENCODE 40.8 +242.4 242412 2.1 FOXA2 ARNT YBX1 ZNF48 TCF12 ZNF416 KLF7 ATF7 FOS SP3 FAM66B MCPH1 MCPH1-AS1 LOC100287015 FAM90A20P ENSG00000271743 AGPAT5 ANGPT2 GC08P006647
GH08H006556 1.8 FANTOM5 Ensembl ENCODE dbSUPER 9.7 +153.5 153518 7.4 ATF1 FOXA2 ARID4B FEZF1 GATA2 KLF7 YY2 TSHZ1 NFIL3 SMARCA4 MCPH1 FAM66B ANGPT2 GC08M006511
GH08H006597 1.5 FANTOM5 Ensembl ENCODE dbSUPER 10.3 +194.4 194397 7 ELF3 SOX13 FOXA2 SAP130 JUN RFX5 GTF3C2 GATA3 SCRT2 EGR2 ANGPT2 MCPH1-AS1 AGPAT5 MCPH1 GC08M006604
GH08H006569 1.3 Ensembl ENCODE dbSUPER 10.3 +163.7 163725 2.3 BCOR HDAC1 TAL1 CEBPG FOSL1 TCF12 ZNF766 GATA2 NCOR1 ADNP AGPAT5 MCPH1-AS1 LOC100287015 MCPH1 ANGPT2 GC08M006604
GH08H006800 1.2 Ensembl ENCODE 10.5 +394.4 394389 0.8 RB1 MLX ARID4B RAD21 RARA GLIS2 EGR1 SCRT2 ZNF143 CREM MCPH1 LOC100287015 PIR35931 GS1-24F4.2
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

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
ENSR00000220546 8 2001 PKNOX1 ATF1 ARID4B SIN3A DMAP1 YY1 GLIS2 ZNF143 ATF7 YY2

Genomic Locations for MCPH1 Gene

Genomic Locations for MCPH1 Gene
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:
    • A0A075B6F8
    • B4DWW2
    • E9PGU5
    • E9PH63
    • Q66GU1
    • Q9H9C7

    Protein attributes for MCPH1 Gene

    835 amino acids
    Molecular mass:
    92849 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

Post-translational modifications for MCPH1 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for MCPH1 Gene

Domains & Families for MCPH1 Gene

Gene Families for MCPH1 Gene

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

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).
genes like me logo Genes that share domains with MCPH1: view

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.

Phenotypes From GWAS Catalog for MCPH1 Gene

Gene Ontology (GO) - Molecular Function for MCPH1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 18660752
GO:0042802 identical protein binding IPI 18660752
genes like me logo Genes that share ontologies with MCPH1: view
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:

miRNA for MCPH1 Gene

miRTarBase miRNAs that target MCPH1

Clone Products

  • Addgene plasmids for MCPH1

No data available for Enzyme Numbers (IUBMB) , 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

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 MCPH1 gene
Compartment Confidence
nucleus 5
cytoskeleton 4
cytosol 3

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nuclear bodies (1)
  • Nucleoplasm (1)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for MCPH1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005654 nucleoplasm TAS --
GO:0005737 cytoplasm IEA --
GO:0005815 microtubule organizing center IEA --
GO:0005856 cytoskeleton IEA --
genes like me logo Genes that share ontologies with MCPH1: view

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:0000122 negative regulation of transcription from RNA polymerase II promoter IDA 12837246
GO:0000132 establishment of mitotic spindle orientation IEA --
GO:0010468 regulation of gene expression IEA --
GO:0021987 cerebral cortex development IEA --
GO:0043549 regulation of kinase activity 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:

Clone Products

  • Addgene plasmids for MCPH1

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 from GTEx, Illumina, BioGPS, and CGAP SAGE 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, MaxQB, and MOPED for MCPH1 Gene

Protein tissue co-expression partners for MCPH1 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of MCPH1 Gene:


SOURCE GeneReport for Unigene cluster for MCPH1 Gene:


mRNA Expression by UniProt/SwissProt for MCPH1 Gene:

Tissue specificity: Expressed in fetal brain, liver and kidney.

Evidence on tissue expression from TISSUES for MCPH1 Gene

  • Nervous system(4.3)
  • Lung(2.8)

Phenotype-based relationships between genes and organs from Gene ORGANizer for MCPH1 Gene

Germ Layers:
  • ectoderm
  • mesoderm
  • integumentary
  • nervous
  • skeletal muscle
  • skeleton
  • urinary
Head and neck:
  • brain
  • cerebellum
  • chin
  • cranial nerve
  • eye
  • eyelid
  • face
  • forehead
  • head
  • jaw
  • lip
  • mandible
  • maxilla
  • mouth
  • neck
  • skull
  • chest wall
  • clavicle
  • rib
  • rib cage
  • scapula
  • sternum
  • kidney
  • pelvis
  • ureter
  • ankle
  • arm
  • digit
  • elbow
  • femur
  • fibula
  • finger
  • foot
  • forearm
  • hand
  • hip
  • humerus
  • knee
  • lower limb
  • radius
  • shin
  • shoulder
  • thigh
  • tibia
  • toe
  • ulna
  • upper limb
  • wrist
  • peripheral nerve
  • peripheral nervous system
  • skin
  • spinal column
  • spinal cord
  • vertebrae
genes like me logo Genes that share expression patterns with MCPH1: view

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
(Pan troglodytes)
Mammalia MCPH1 33 34
  • 98.96 (n)
(Canis familiaris)
Mammalia MCPH1 33 34
  • 75.03 (n)
(Monodelphis domestica)
Mammalia -- 34
  • 72 (a)
-- 34
  • 63 (a)
-- 34
  • 27 (a)
(Rattus norvegicus)
Mammalia Mcph1 33
  • 71.6 (n)
(Mus musculus)
Mammalia Mcph1 33 16 34
  • 71.45 (n)
(Bos Taurus)
Mammalia MCPH1 33 34
  • 67.91 (n)
(Ornithorhynchus anatinus)
Mammalia -- 34
  • 52 (a)
-- 34
  • 36 (a)
(Gallus gallus)
Aves MCPH1 33 34
  • 65.13 (n)
(Anolis carolinensis)
Reptilia MCPH1 34
  • 58 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia Str.17324 33
(Danio rerio)
Actinopterygii mcph1 34
  • 46 (a)
Dr.15463 33
fruit fly
(Drosophila melanogaster)
Insecta MCPH1 34
  • 16 (a)
sea squirt
(Ciona savignyi)
Ascidiacea CSA.10623 34
  • 23 (a)
Species where no ortholog for MCPH1 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)
  • 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
rs199422124 Pathogenic, Microcephaly 1, primary, autosomal recessive (MCPH1) [MIM:251200] 6,409,336(+) AAAGA(C/G)ATTTA nc-transcript-variant, reference, missense, utr-variant-5-prime
rs121434305 Pathogenic 6,409,330(+) TTATT(C/G)AAAGA nc-transcript-variant, reference, stop-gained, utr-variant-5-prime
rs199422125 Pathogenic 6,436,153(+) AAAAA(-/A)CAAAT intron-variant, nc-transcript-variant, reference, frameshift-variant
rs201599657 Pathogenic 6,499,860(+) CTATG(A/G)TCTTT intron-variant, nc-transcript-variant, downstream-variant-500B, reference, utr-variant-3-prime, stop-gained
rs387906961 Pathogenic 6,414,865(+) CGTTT(C/T)GGTGC nc-transcript-variant, reference, missense

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

Variant ID Type Subtype PubMed ID
nsv958484 CNV deletion 24416366
nsv610005 CNV gain 21841781
nsv610004 CNV gain 21841781
nsv6058 CNV insertion 18451855
nsv6057 CNV insertion 18451855
nsv527005 CNV gain 19592680
nsv526417 CNV loss 19592680
nsv524670 CNV loss 19592680
nsv524404 CNV loss 19592680
nsv522043 CNV loss 19592680
nsv521585 CNV loss 19592680
nsv397733 CNV deletion 16902084
nsv1161706 CNV duplication 26073780
nsv1124316 CNV deletion 24896259
nsv1033935 CNV loss 25217958
nsv1030323 CNV loss 25217958
nsv1025976 CNV loss 25217958
nsv1025860 CNV loss 25217958
nsv1024024 CNV gain 25217958
nsv1023443 CNV loss 25217958
nsv1022895 CNV loss 25217958
nsv1021684 CNV loss 25217958
nsv1018882 CNV loss 25217958
nsv1018782 CNV loss 25217958
esv3891314 CNV gain 25118596
esv3616097 CNV gain 21293372
esv3616094 CNV gain 21293372
esv3616093 CNV loss 21293372
esv3616092 CNV gain 21293372
esv3576515 CNV gain 25503493
esv3398137 CNV insertion 20981092
esv2761219 CNV loss 21179565
esv2736534 CNV deletion 23290073
esv2736533 CNV deletion 23290073
esv2736532 CNV deletion 23290073
esv2736531 CNV deletion 23290073
esv2736530 CNV deletion 23290073
esv2668625 CNV deletion 23128226
esv2422383 CNV duplication 17116639
esv1010135 CNV insertion 20482838
dgv6868n100 CNV gain 25217958
dgv444n21 CNV loss 19592680
dgv443n21 CNV loss 19592680
dgv2029e212 CNV loss 25503493
dgv1364e214 CNV loss 21293372

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)
SNPedia medical, phenotypic, and genealogical associations of SNPs for

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

Disorders for MCPH1 Gene

MalaCards: The human disease database

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

Disorder Aliases PubMed IDs
microcephaly 1, primary, autosomal recessive
  • primary autosomal recessive microcephaly type 1
primary microcephaly
  • microcephaly, primary
  • microcephalus
congenital nervous system abnormality
  • congenital neurologic anomaly
seckel syndrome
  • bird-headed dwarfism
- 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. Sex-dependent association of common variants of microcephaly genes with brain structure. (PMID: 20080800) Rimol LM … Alzheimer's Disease Neuroimaging Initiative (Proceedings of the National Academy of Sciences of the United States of America 2010) 3 22 45 60
  2. The c.940G variant of the Microcephalin (MCPH1) gene is not associated with microcephaly or mental retardation. (PMID: 19267414) Maghirang-Rodriguez R … Collins JS (American journal of medical genetics. Part A 2009) 3 22 45 60
  3. A common SNP of MCPH1 is associated with cranial volume variation in Chinese population. (PMID: 18204051) Wang JK … Su B (Human molecular genetics 2008) 3 4 45 60
  4. MCPH1 functions in an H2AX-dependent but MDC1-independent pathway in response to DNA damage. (PMID: 17925396) Wood JL … Chen J (The Journal of biological chemistry 2007) 2 3 22 60
  5. Microcephalin encodes a centrosomal protein. (PMID: 16479174) Zhong X … Xu X (Cell cycle (Georgetown, Tex.) 2006) 3 4 22 60

Products for MCPH1 Gene

Sources for MCPH1 Gene

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