MCPH1 microcephalin 1 [Homo sapiens (human)] - Gene

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: mouse all
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Genomic context

Location:: 8p23.1

Exon count:: 23

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	8	NC_000008.11 (6406627..6648508)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	8	NC_060932.1 (6161207..6402976)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	8	NC_000008.10 (6264148..6506029)

Chromosome 8 - NC_000008.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues 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

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

MCPH1: A Novel Case Report and a Review of the Literature.
Title: MCPH1: A Novel Case Report and a Review of the Literature.
Identification of Pathogenic Mutations in Primary Microcephaly- (MCPH-) Related Three Genes CENPJ, CASK, and MCPH1 in Consanguineous Pakistani Families.
Title: Identification of Pathogenic Mutations in Primary Microcephaly- (MCPH-) Related Three Genes CENPJ, CASK, and MCPH1 in Consanguineous Pakistani Families.
MCPH1, beyond its role deciding the brain size.
Title: MCPH1, beyond its role deciding the brain size.
Tone and genes: New cross-linguistic data and methods support the weak negative effect of the ""derived"" allele of ASPM on tone, but not of Microcephalin.
Title: Tone and genes: New cross-linguistic data and methods support the weak negative effect of the "derived" allele of ASPM on tone, but not of Microcephalin.
Investigation of promoter methylation of MCPH1 gene in circulating cell-free DNA of brain tumor patients.
Title: Investigation of promoter methylation of MCPH1 gene in circulating cell-free DNA of brain tumor patients.
BRIT-1 expression and its relationship with PARP-1 and CAF-1/p60 in cutaneous melanoma.
Title: BRIT-1 expression and its relationship with PARP-1 and CAF-1/p60 in cutaneous melanoma.
Cell Metabolic Alterations due to Mcph1 Mutation in Microcephaly.
Title: Cell Metabolic Alterations due to Mcph1 Mutation in Microcephaly.
MCPH1 Lack of Function Enhances Mitotic Cell Sensitivity Caused by Catalytic Inhibitors of Topo II.
Title: MCPH1 Lack of Function Enhances Mitotic Cell Sensitivity Caused by Catalytic Inhibitors of Topo II.
Microcephalin 1/BRIT1-TRF2 interaction promotes telomere replication and repair, linking telomere dysfunction to primary microcephaly.
Title: Microcephalin 1/BRIT1-TRF2 interaction promotes telomere replication and repair, linking telomere dysfunction to primary microcephaly.
Analysis of the ""centrosome-ome"" identifies MCPH1 deletion as a cause of centrosome amplification in human cancer.
Title: Analysis of the "centrosome-ome" identifies MCPH1 deletion as a cause of centrosome amplification in human cancer.

Submit: New GeneRIF Correction See all GeneRIFs (83)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

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 EBI GWAS CatalogPubMed
Genome-wide association study does not reveal major genetic determinants for anti-cytomegalovirus antibody response. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association study of epirubicin-induced leukopenia in Japanese patients. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

WIAF-2168 (e-PCR)
- UniSTS:71682

G19225 (e-PCR)
- UniSTS:5892

SHGC-148851 (e-PCR)
- UniSTS:176645

D11S2921 (e-PCR)
- UniSTS:152074

SHGC-142612 (e-PCR)
- UniSTS:171549

STS-AA011655 (e-PCR)
- UniSTS:46128

RH48380 (e-PCR)
- UniSTS:40532

RH121218 (e-PCR)
- UniSTS:138329

RH69270 (e-PCR)
- UniSTS:39001

RH93262 (e-PCR)
- UniSTS:84317

D10S16 (e-PCR)
- UniSTS:155756

G66160 (e-PCR)
- UniSTS:229996

SHGC-36472 (e-PCR)
- UniSTS:70278

RH120360 (e-PCR)
- UniSTS:132501

D8S1413E (e-PCR)
- UniSTS:56472

D8S2077 (e-PCR)
- UniSTS:70809

RH47768 (e-PCR)
- UniSTS:71068

RH75428 (e-PCR)
- UniSTS:84388

A004X20 (e-PCR)
- UniSTS:60844

SHGC-77726 (e-PCR)
- UniSTS:95929

SHGC-84494 (e-PCR)
- UniSTS:102842

G59875 (e-PCR)
- UniSTS:137158

D8S1935 (e-PCR)
- UniSTS:39908

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

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Preferred Names: microcephalin

Names: BRCT-repeat inhibitor of TERT expression 1

NCBI Reference Sequences (RefSeq)

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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

NG_016619.3 RefSeqGene

Range

5002..246883

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001172574.2 → NP_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:8 → 86

BRCT_microcephalin_rpt1; first (N-terminal) BRCT domain of microcephalin and similar proteins

pfam12258
Location:225 → 607

Microcephalin; Microcephalin protein
NM_001172575.2 → NP_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:179 → 555

Microcephalin; Microcephalin protein

pfam12738
Location:9 → 75

PTCB-BRCT; twin BRCT domain
NM_001322042.2 → NP_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:8 → 86

BRCT_microcephalin_rpt1; first (N-terminal) BRCT domain of microcephalin and similar proteins

cd17736
Location:648 → 723

BRCT_microcephalin_rpt2; second BRCT domain of microcephalin and similar proteins

cd17751
Location:749 → 824

BRCT_microcephalin_rpt3; third BRCT domain of microcephalin and similar proteins

pfam12258
Location:227 → 603

Microcephalin; Microcephalin protein
NM_001322043.2 → NP_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:8 → 84

BRCT_microcephalin_rpt1; first (N-terminal) BRCT domain of microcephalin and similar proteins

pfam12258
Location:223 → 605

Microcephalin; Microcephalin protein
NM_001322045.2 → NP_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:1 → 52

BRCT_microcephalin_rpt1; first (N-terminal) BRCT domain of microcephalin and similar proteins

pfam12258
Location:191 → 573

Microcephalin; Microcephalin protein
NM_001363979.1 → NP_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:669 → 714

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:227 → 603

Microcephalin; Microcephalin protein

pfam12738
Location:9 → 75

PTCB-BRCT; twin BRCT domain
NM_001363980.2 → NP_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:227 → 603

Microcephalin; Microcephalin protein

pfam12738
Location:9 → 75

PTCB-BRCT; twin BRCT domain

cl00038
Location:670 → 739

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 ...
NM_001410916.1 → NP_001397845.1 microcephalin isoform 9

Status: REVIEWED

Source sequence(s)

AC016065, AC018398

Consensus CDS

CCDS94245.1

UniProtKB/TrEMBL

A0A8I5KZ89

Related

ENSP00000510652.1, ENST00000691435.1
NM_001410917.1 → NP_001397846.1 microcephalin isoform 10

Status: REVIEWED

Source sequence(s)

AC016065, AC018398, AF287957

Consensus CDS

CCDS94247.1

UniProtKB/TrEMBL

A0A8I5KPV6

Related

ENSP00000509072.1, ENST00000692938.1
NM_024596.5 → NP_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:669 → 714

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:227 → 603

Microcephalin; Microcephalin protein

pfam12738
Location:9 → 75

PTCB-BRCT; twin BRCT domain

cl00038
Location:763 → 832

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

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_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000008.11 Reference GRCh38.p14 Primary Assembly

Range

6406627..6648508

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_017013833.3 → XP_016869322.1 microcephalin isoform X7

UniProtKB/TrEMBL

A0A8I5QKY7
XM_047422234.1 → XP_047278190.1 microcephalin isoform X5
XM_047422233.1 → XP_047278189.1 microcephalin isoform X2

Related

ENSP00000510092.1, ENST00000688388.1
XM_017013829.3 → XP_016869318.1 microcephalin isoform X1

UniProtKB/TrEMBL

A0A8I5KX36
XM_017013832.3 → XP_016869321.1 microcephalin isoform X3

UniProtKB/TrEMBL

A0A8I5QKY7
XM_011534757.4 → XP_011533059.1 microcephalin isoform X6

UniProtKB/TrEMBL

A0A8I5QKY7

Conserved Domains (3) summary

cd00027
Location:669 → 714

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:227 → 603

Microcephalin; Microcephalin protein

pfam12738
Location:9 → 75

PTCB-BRCT; twin BRCT domain
XM_011534756.4 → XP_011533058.1 microcephalin isoform X4

UniProtKB/TrEMBL

A0A8I5QKY7

Related

ENST00000688912.1

Conserved Domains (3) summary

cd00027
Location:669 → 714

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:227 → 603

Microcephalin; Microcephalin protein

pfam12738
Location:9 → 75

PTCB-BRCT; twin BRCT domain
XM_011534758.4 → XP_011533060.1 microcephalin isoform X8

UniProtKB/TrEMBL

A0A8I5QKY7

Conserved Domains (3) summary

cd00027
Location:669 → 714

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:227 → 603

Microcephalin; Microcephalin protein

pfam12738
Location:9 → 75

PTCB-BRCT; twin BRCT domain