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    MCPH1 microcephalin 1 [ Homo sapiens (human) ]

    Gene ID: 79648, updated on 6-Jun-2024

    Summary

    Official Symbol
    MCPH1provided by HGNC
    Official Full Name
    microcephalin 1provided by HGNC
    Primary source
    HGNC:HGNC:6954
    See related
    Ensembl:ENSG00000147316 MIM:607117; AllianceGenome:HGNC:6954
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    MCT; BRIT1
    Summary
    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]
    Expression
    Ubiquitous expression in bone marrow (RPKM 1.3), testis (RPKM 1.1) and 25 other tissues See more
    Orthologs
    NEW
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    Genomic context

    See MCPH1 in Genome Data Viewer
    Location:
    8p23.1
    Exon count:
    23
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 8 NC_000008.11 (6406627..6648508)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 8 NC_060932.1 (6161207..6402976)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 8 NC_000008.10 (6264148..6506029)

    Chromosome 8 - NC_000008.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105377797 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_103459 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr8:6170563-6171762 Neighboring gene NANOG hESC enhancer GRCh37_chr8:6189146-6189652 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr8:6247558-6248757 Neighboring gene MPRA-validated peak6892 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18880 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18881 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26946 Neighboring gene Sharpr-MPRA regulatory region 14576 Neighboring gene MCPH1 divergent transcript Neighboring gene adenylate kinase isoenzyme 6-like Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr8:6385720-6386919 Neighboring gene angiopoietin 2 Neighboring gene Sharpr-MPRA regulatory region 12768 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:6419583-6420108 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:6420109-6420635 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:6434138-6434684 Neighboring gene ReSE screen-validated silencer GRCh37_chr8:6436241-6436413 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_103492 Neighboring gene H3K27ac hESC enhancer GRCh37_chr8:6446215-6446714 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:6451447-6452362 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:6450530-6451446 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr8:6456108-6457307 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:6459927-6460426 Neighboring gene NANOG hESC enhancer GRCh37_chr8:6473596-6474097 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:6481178-6481678 Neighboring gene MCPH1 antisense RNA 1 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr8:6505663-6506862 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18882 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26948 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26949 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26950 Neighboring gene microRNA 8055 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26951 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26952 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18883 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18884 Neighboring gene protein tyrosine phosphatase non-receptor type 4 pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18885 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26953 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26954 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26955 Neighboring gene 1-acylglycerol-3-phosphate O-acyltransferase 5 Neighboring gene microRNA 4659a Neighboring gene microRNA 4659b

    Genomic regions, transcripts, and products

    Expression

    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    Associated conditions

    Description Tests
    Microcephaly 1, primary, autosomal recessive
    MedGen: C1855081 OMIM: 251200 GeneReviews: Not available
    Compare labs

    EBI GWAS Catalog

    Description
    Discovery of genetic biomarkers contributing to variation in drug response of cytidine analogues using human lymphoblastoid cell lines.
    EBI GWAS Catalog
    Genome-wide association study does not reveal major genetic determinants for anti-cytomegalovirus antibody response.
    EBI GWAS Catalog
    Genome-wide association study of epirubicin-induced leukopenia in Japanese patients.
    EBI GWAS Catalog

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • FLJ12847

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables identical protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    Process Evidence Code Pubs
    involved_in bone development IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in cerebral cortex development IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in establishment of mitotic spindle orientation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in mitotic cell cycle IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in negative regulation of transcription by RNA polymerase II IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in neuronal stem cell population maintenance IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in protein localization to centrosome IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in regulation of centrosome cycle IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in regulation of chromosome condensation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in regulation of inflammatory response IEA
    Inferred from Electronic Annotation
    more info
     
    Component Evidence Code Pubs
    located_in centrosome IEA
    Inferred from Electronic Annotation
    more info
     
    located_in cytoplasm IEA
    Inferred from Electronic Annotation
    more info
     
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
     

    General protein information

    Preferred Names
    microcephalin
    Names
    BRCT-repeat inhibitor of TERT expression 1

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    Genomic

    1. NG_016619.3 RefSeqGene

      Range
      5002..246883
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001172574.2NP_001166045.2  microcephalin isoform 2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2, also known as MCPH1deltae9-14) differs in the 3' coding region and 3' UTR, compared to variant 1. The resulting isoform (2) has a distinct C-terminus and is shorter than isoform 1.
      Source sequence(s)
      AC016065
      Consensus CDS
      CCDS55190.1
      UniProtKB/TrEMBL
      A0A8I5KRI7
      Related
      ENSP00000430962.1, ENST00000519480.6
      Conserved Domains (2) summary
      cd17716
      Location:886
      BRCT_microcephalin_rpt1; first (N-terminal) BRCT domain of microcephalin and similar proteins
      pfam12258
      Location:225607
      Microcephalin; Microcephalin protein
    2. NM_001172575.2NP_001166046.1  microcephalin isoform 3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) lacks an in-frame exon in the 5' coding region, and differs in the 3' coding region and 3' UTR, compared to variant 1. The resulting isoform (3) has a distinct C-terminus and is shorter than isoform 1.
      Source sequence(s)
      AC016065, AI379664, AK301702, BC030702
      Consensus CDS
      CCDS55191.1
      UniProtKB/TrEMBL
      A0A8I5KRI7
      Related
      ENSP00000430768.1, ENST00000522905.1
      Conserved Domains (2) summary
      pfam12258
      Location:179555
      Microcephalin; Microcephalin protein
      pfam12738
      Location:975
      PTCB-BRCT; twin BRCT domain
    3. NM_001322042.2NP_001308971.2  microcephalin isoform 4

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) contains an additional exon that results in a frameshift in the 3' coding region, compared to variant 1. The encoded isoform (4) has a distinct C-terminus and is longer than isoform 1.
      Source sequence(s)
      AC016065, AC018398, AF287957
      Consensus CDS
      CCDS94246.1
      UniProtKB/TrEMBL
      A0A8I5KV10, A0A8I5KX36
      Related
      ENSP00000509554.1, ENST00000689348.1
      Conserved Domains (4) summary
      cd17716
      Location:886
      BRCT_microcephalin_rpt1; first (N-terminal) BRCT domain of microcephalin and similar proteins
      cd17736
      Location:648723
      BRCT_microcephalin_rpt2; second BRCT domain of microcephalin and similar proteins
      cd17751
      Location:749824
      BRCT_microcephalin_rpt3; third BRCT domain of microcephalin and similar proteins
      pfam12258
      Location:227603
      Microcephalin; Microcephalin protein
    4. NM_001322043.2NP_001308972.2  microcephalin isoform 5

      Status: REVIEWED

      Description
      Transcript Variant: This variant (5) uses an alternate in-frame splice site in the 5' coding region, and lacks several 3' exons but contains an alternate 3' terminal exon and thus differs in the 3' coding region and 3' UTR, compared to variant 1. The encoded isoform (5) has a distinct C-terminus and is shorter than isoform 1.
      Source sequence(s)
      AC016065
      Consensus CDS
      CCDS94250.1
      UniProtKB/TrEMBL
      A0A8I5KR64, A0A8I5KRI7
      Related
      ENSP00000510001.1, ENST00000685179.1
      Conserved Domains (2) summary
      cd17716
      Location:884
      BRCT_microcephalin_rpt1; first (N-terminal) BRCT domain of microcephalin and similar proteins
      pfam12258
      Location:223605
      Microcephalin; Microcephalin protein
    5. NM_001322045.2NP_001308974.2  microcephalin isoform 6

      Status: REVIEWED

      Description
      Transcript Variant: This variant (6) contains an alternate 5' terminal exon and it thus differs in the 5' UTR and initiates translation from a downstream in-frame start codon, and it also lacks several 3' exons but contains an alternate 3' terminal exon and thus differs in the 3' coding region and 3' UTR, compared to variant 1. The encoded isoform (6) is shorter at the N-terminus and has a distinct and shorter C-terminus, compared to isoform 1.
      Source sequence(s)
      AC016065
      UniProtKB/TrEMBL
      A0A8I5KRI7
      Conserved Domains (2) summary
      cd17716
      Location:152
      BRCT_microcephalin_rpt1; first (N-terminal) BRCT domain of microcephalin and similar proteins
      pfam12258
      Location:191573
      Microcephalin; Microcephalin protein
    6. NM_001363979.1NP_001350908.1  microcephalin isoform 7

      Status: REVIEWED

      Source sequence(s)
      AC016065, AC018398, AF287957
      Consensus CDS
      CCDS94248.1
      UniProtKB/TrEMBL
      A0A8I5KW78, A0A8I5KX36
      Related
      ENSP00000510536.1, ENST00000690826.1
      Conserved Domains (3) summary
      cd00027
      Location:669714
      BRCT; Breast Cancer Suppressor Protein (BRCA1), carboxy-terminal domain. The BRCT domain is found within many DNA damage repair and cell cycle checkpoint proteins. The unique diversity of this domain superfamily allows BRCT modules to interact forming homo ...
      pfam12258
      Location:227603
      Microcephalin; Microcephalin protein
      pfam12738
      Location:975
      PTCB-BRCT; twin BRCT domain
    7. NM_001363980.2NP_001350909.1  microcephalin isoform 8

      Status: REVIEWED

      Source sequence(s)
      AC016065, AF287957
      Consensus CDS
      CCDS94249.1
      UniProtKB/TrEMBL
      A0A8I5KR97, A0A8I5QKY7
      Related
      ENSP00000509054.1, ENST00000689633.1
      Conserved Domains (3) summary
      pfam12258
      Location:227603
      Microcephalin; Microcephalin protein
      pfam12738
      Location:975
      PTCB-BRCT; twin BRCT domain
      cl00038
      Location:670739
      BRCT; Breast Cancer Suppressor Protein (BRCA1), carboxy-terminal domain. The BRCT domain is found within many DNA damage repair and cell cycle checkpoint proteins. The unique diversity of this domain superfamily allows BRCT modules to interact forming homo ...
    8. NM_001410916.1NP_001397845.1  microcephalin isoform 9

      Status: REVIEWED

      Source sequence(s)
      AC016065, AC018398
      Consensus CDS
      CCDS94245.1
      UniProtKB/TrEMBL
      A0A8I5KZ89, A0A8I5QKY7
      Related
      ENSP00000510652.1, ENST00000691435.1
    9. NM_001410917.1NP_001397846.1  microcephalin isoform 10

      Status: REVIEWED

      Source sequence(s)
      AC016065, AC018398, AF287957
      Consensus CDS
      CCDS94247.1
      UniProtKB/TrEMBL
      A0A8I5KPV6, A0A8I5KX36
      Related
      ENSP00000509072.1, ENST00000692938.1
    10. NM_024596.5NP_078872.3  microcephalin isoform 1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1, also known as MCPH1-FL) encodes isoform 1.
      Source sequence(s)
      AC016065, AC018398, AF287957
      Consensus CDS
      CCDS43689.1
      UniProtKB/Swiss-Prot
      A0A075B6F8, B4DWW2, E9PGU5, E9PH63, Q66GU1, Q8NEM0, Q9H9C7
      UniProtKB/TrEMBL
      A0A8I5KX36
      Related
      ENSP00000342924.5, ENST00000344683.10
      Conserved Domains (4) summary
      cd00027
      Location:669714
      BRCT; Breast Cancer Suppressor Protein (BRCA1), carboxy-terminal domain. The BRCT domain is found within many DNA damage repair and cell cycle checkpoint proteins. The unique diversity of this domain superfamily allows BRCT modules to interact forming homo ...
      pfam12258
      Location:227603
      Microcephalin; Microcephalin protein
      pfam12738
      Location:975
      PTCB-BRCT; twin BRCT domain
      cl00038
      Location:763832
      BRCT; Breast Cancer Suppressor Protein (BRCA1), carboxy-terminal domain. The BRCT domain is found within many DNA damage repair and cell cycle checkpoint proteins. The unique diversity of this domain superfamily allows BRCT modules to interact forming homo ...

    RNA

    1. NR_136159.2 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (7) lacks an internal exon and several 3' exons, but contains an alternate 3' terminal exon, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AC016065

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000008.11 Reference GRCh38.p14 Primary Assembly

      Range
      6406627..6648508
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017013833.3XP_016869322.1  microcephalin isoform X7

      UniProtKB/TrEMBL
      A0A8I5QKY7
    2. XM_047422234.1XP_047278190.1  microcephalin isoform X5

      UniProtKB/TrEMBL
      A0A8I5KX36
    3. XM_047422233.1XP_047278189.1  microcephalin isoform X2

      UniProtKB/TrEMBL
      A0A8I5KX36
      Related
      ENSP00000510092.1, ENST00000688388.1
    4. XM_017013829.3XP_016869318.1  microcephalin isoform X1

      UniProtKB/TrEMBL
      A0A8I5KX36
    5. XM_017013832.3XP_016869321.1  microcephalin isoform X3

      UniProtKB/TrEMBL
      A0A8I5QKY7
    6. XM_011534757.4XP_011533059.1  microcephalin isoform X6

      UniProtKB/TrEMBL
      A0A8I5QKY7
      Conserved Domains (3) summary
      cd00027
      Location:669714
      BRCT; Breast Cancer Suppressor Protein (BRCA1), carboxy-terminal domain. The BRCT domain is found within many DNA damage repair and cell cycle checkpoint proteins. The unique diversity of this domain superfamily allows BRCT modules to interact forming homo ...
      pfam12258
      Location:227603
      Microcephalin; Microcephalin protein
      pfam12738
      Location:975
      PTCB-BRCT; twin BRCT domain
    7. XM_011534756.4XP_011533058.1  microcephalin isoform X4

      UniProtKB/TrEMBL
      A0A8I5QKY7
      Related
      ENST00000688912.1
      Conserved Domains (3) summary
      cd00027
      Location:669714
      BRCT; Breast Cancer Suppressor Protein (BRCA1), carboxy-terminal domain. The BRCT domain is found within many DNA damage repair and cell cycle checkpoint proteins. The unique diversity of this domain superfamily allows BRCT modules to interact forming homo ...
      pfam12258
      Location:227603
      Microcephalin; Microcephalin protein
      pfam12738
      Location:975
      PTCB-BRCT; twin BRCT domain
    8. XM_011534758.4XP_011533060.1  microcephalin isoform X8

      UniProtKB/TrEMBL
      A0A8I5QKY7
      Conserved Domains (3) summary
      cd00027
      Location:669714
      BRCT; Breast Cancer Suppressor Protein (BRCA1), carboxy-terminal domain. The BRCT domain is found within many DNA damage repair and cell cycle checkpoint proteins. The unique diversity of this domain superfamily allows BRCT modules to interact forming homo ...
      pfam12258
      Location:227603
      Microcephalin; Microcephalin protein
      pfam12738
      Location:975
      PTCB-BRCT; twin BRCT domain

    Reference GRCh38.p14 PATCHES

    Genomic

    1. NW_018654717.1 Reference GRCh38.p14 PATCHES

      Range
      8385..43778
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Reference GRCh38.p14 PATCHES

    Genomic

    1. NW_025791785.1 Reference GRCh38.p14 PATCHES

      Range
      342105..416356
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060932.1 Alternate T2T-CHM13v2.0

      Range
      6161207..6402976
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054361230.1XP_054217205.1  microcephalin isoform X7

      UniProtKB/TrEMBL
      A0A1B2M4G2
    2. XM_054361228.1XP_054217203.1  microcephalin isoform X5

      UniProtKB/TrEMBL
      A0A8I5KX36
    3. XM_054361225.1XP_054217200.1  microcephalin isoform X2

      UniProtKB/TrEMBL
      A0A8I5KX36
    4. XM_054361224.1XP_054217199.1  microcephalin isoform X1

      UniProtKB/TrEMBL
      A0A8I5KX36
    5. XM_054361226.1XP_054217201.1  microcephalin isoform X3

      UniProtKB/TrEMBL
      A0A1B2M4G2
    6. XM_054361227.1XP_054217202.1  microcephalin isoform X4

      UniProtKB/TrEMBL
      A0A1B2M4G2
    7. XM_054361229.1XP_054217204.1  microcephalin isoform X6

      UniProtKB/TrEMBL
      A0A1B2M4G2
    8. XM_054361231.1XP_054217206.1  microcephalin isoform X8

      UniProtKB/TrEMBL
      A0A1B2M4G2