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MDC1 mediator of DNA damage checkpoint 1 [ Homo sapiens (human) ]

Gene ID: 9656, updated on 8-Jan-2023

Summary

Official Symbol
MDC1provided by HGNC
Official Full Name
mediator of DNA damage checkpoint 1provided by HGNC
Primary source
HGNC:HGNC:21163
See related
Ensembl:ENSG00000137337 MIM:607593; AllianceGenome:HGNC:21163
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
NFBD1
Summary
The protein encoded by this gene contains an N-terminal forkhead domain, two BRCA1 C-terminal (BRCT) motifs and a central domain with 13 repetitions of an approximately 41-amino acid sequence. The encoded protein is required to activate the intra-S phase and G2/M phase cell cycle checkpoints in response to DNA damage. This nuclear protein interacts with phosphorylated histone H2AX near sites of DNA double-strand breaks through its BRCT motifs, and facilitates recruitment of the ATM kinase and meiotic recombination 11 protein complex to DNA damage foci. [provided by RefSeq, Jul 2008]
Expression
Broad expression in testis (RPKM 20.6), thyroid (RPKM 7.4) and 25 other tissues See more
Orthologs
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Genomic context

See MDC1 in Genome Data Viewer
Location:
6p21.33
Exon count:
17
Annotation release Status Assembly Chr Location
110 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (30699807..30717281, complement)
110 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (30564011..30581484, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (30667584..30685058, complement)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene protein phosphatase 1 regulatory subunit 18 Neighboring gene nurim Neighboring gene ribosomal protein L7 pseudogene 4 Neighboring gene MDC1 antisense RNA 1 Neighboring gene tubulin beta class I Neighboring gene flotillin 1

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

EBI GWAS Catalog

Description
Loci associated with N-glycosylation of human immunoglobulin G show pleiotropy with autoimmune diseases and haematological cancers.
EBI GWAS Catalog

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • KIAA0170, MGC166888, DKFZp781A0122

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables FHA domain 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 DNA repair IEA
Inferred from Electronic Annotation
more info
 
involved_in mitotic intra-S DNA damage checkpoint signaling TAS
Traceable Author Statement
more info
PubMed 
involved_in positive regulation of transcription initiation by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Component Evidence Code Pubs
located_in chromosome ISS
Inferred from Sequence or Structural Similarity
more info
 
located_in focal adhesion IDA
Inferred from Direct Assay
more info
 
located_in nuclear body IDA
Inferred from Direct Assay
more info
 
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
 
located_in nucleoplasm TAS
Traceable Author Statement
more info
 
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
located_in nucleus IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
mediator of DNA damage checkpoint protein 1
Names
homologue to Drosophila photoreceptor protein calphotin
nuclear factor with BRCT domains 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.

mRNA and Protein(s)

  1. NM_014641.3NP_055456.2  mediator of DNA damage checkpoint protein 1

    See identical proteins and their annotated locations for NP_055456.2

    Status: REVIEWED

    Source sequence(s)
    AL662797, BU621433, D79992, EF177823
    Consensus CDS
    CCDS34384.1
    UniProtKB/Swiss-Prot
    Q14676, Q96QC2
    UniProtKB/TrEMBL
    A0A1U9XBC1, A1Z5I9
    Related
    ENSP00000365588.3, ENST00000376406.8
    Conserved Domains (5) summary
    pfam00498
    Location:55110
    FHA; FHA domain
    cl00038
    Location:18821968
    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 ...
    cl25732
    Location:822962
    SMC_N; RecF/RecN/SMC N terminal domain
    cl25751
    Location:9431376
    DUF4045; Domain of unknown function (DUF4045)
    cl26464
    Location:12271757
    Atrophin-1; Atrophin-1 family

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 110 details...Open this link in a new tab

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000006.12 Reference GRCh38.p14 Primary Assembly

    Range
    30699807..30717281 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047419589.1XP_047275545.1  mediator of DNA damage checkpoint protein 1 isoform X11

  2. XM_047419588.1XP_047275544.1  mediator of DNA damage checkpoint protein 1 isoform X10

  3. XM_047419586.1XP_047275542.1  mediator of DNA damage checkpoint protein 1 isoform X7

  4. XM_005249494.6XP_005249551.1  mediator of DNA damage checkpoint protein 1 isoform X3

    See identical proteins and their annotated locations for XP_005249551.1

    UniProtKB/Swiss-Prot
    Q14676, Q96QC2
    UniProtKB/TrEMBL
    A0A1U9XBC1
    Conserved Domains (5) summary
    pfam00498
    Location:55110
    FHA; FHA domain
    cl00038
    Location:18821968
    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 ...
    cl25732
    Location:822962
    SMC_N; RecF/RecN/SMC N terminal domain
    cl25751
    Location:9431376
    DUF4045; Domain of unknown function (DUF4045)
    cl26464
    Location:12271757
    Atrophin-1; Atrophin-1 family
  5. XM_047419582.1XP_047275538.1  mediator of DNA damage checkpoint protein 1 isoform X3

    UniProtKB/Swiss-Prot
    Q96QC2
    UniProtKB/TrEMBL
    A0A1U9XBC1
  6. XM_047419584.1XP_047275540.1  mediator of DNA damage checkpoint protein 1 isoform X3

    UniProtKB/Swiss-Prot
    Q96QC2
    UniProtKB/TrEMBL
    A0A1U9XBC1
  7. XM_017011522.3XP_016867011.1  mediator of DNA damage checkpoint protein 1 isoform X9

  8. XM_047419585.1XP_047275541.1  mediator of DNA damage checkpoint protein 1 isoform X6

  9. XM_047419581.1XP_047275537.1  mediator of DNA damage checkpoint protein 1 isoform X2

  10. XM_047419587.1XP_047275543.1  mediator of DNA damage checkpoint protein 1 isoform X8

  11. XM_047419580.1XP_047275536.1  mediator of DNA damage checkpoint protein 1 isoform X1

  12. XM_047419583.1XP_047275539.1  mediator of DNA damage checkpoint protein 1 isoform X3

    UniProtKB/Swiss-Prot
    Q96QC2
    UniProtKB/TrEMBL
    A0A1U9XBC1
  13. XM_011515003.4XP_011513305.1  mediator of DNA damage checkpoint protein 1 isoform X3

    See identical proteins and their annotated locations for XP_011513305.1

    UniProtKB/Swiss-Prot
    Q14676, Q96QC2
    UniProtKB/TrEMBL
    A0A1U9XBC1
    Conserved Domains (5) summary
    pfam00498
    Location:55110
    FHA; FHA domain
    cl00038
    Location:18821968
    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 ...
    cl25732
    Location:822962
    SMC_N; RecF/RecN/SMC N terminal domain
    cl25751
    Location:9431376
    DUF4045; Domain of unknown function (DUF4045)
    cl26464
    Location:12271757
    Atrophin-1; Atrophin-1 family
  14. XM_005249498.5XP_005249555.1  mediator of DNA damage checkpoint protein 1 isoform X8

    See identical proteins and their annotated locations for XP_005249555.1

    Conserved Domains (2) summary
    cd00027
    Location:16631715
    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 ...
    pfam00498
    Location:76144
    FHA; FHA domain
  15. XM_005249497.5XP_005249554.1  mediator of DNA damage checkpoint protein 1 isoform X5

    See identical proteins and their annotated locations for XP_005249554.1

    Conserved Domains (2) summary
    cd00027
    Location:17371789
    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 ...
    pfam00498
    Location:76144
    FHA; FHA domain
  16. XM_005249492.3XP_005249549.1  mediator of DNA damage checkpoint protein 1 isoform X1

    See identical proteins and their annotated locations for XP_005249549.1

    Conserved Domains (6) summary
    PTZ00449
    Location:9641397
    PTZ00449; 104 kDa microneme/rhoptry antigen; Provisional
    PHA03247
    Location:12481778
    PHA03247; large tegument protein UL36; Provisional
    cd00060
    Location:54144
    FHA; Forkhead associated domain (FHA); found in eukaryotic and prokaryotic proteins. Putative nuclear signalling domain. FHA domains may bind phosphothreonine, phosphoserine and sometimes phosphotyrosine. In eukaryotes, many FHA domain-containing proteins ...
    TIGR02169
    Location:843983
    SMC_prok_A; chromosome segregation protein SMC, primarily archaeal type
    cd17744
    Location:19141984
    BRCT_MDC1_rpt1; first BRCT domain of mediator of DNA damage checkpoint protein 1 (MDC1) and similar proteins
    cd18441
    Location:20162096
    BRCT_MDC1_rpt2; second BRCT domain of mediator of DNA damage checkpoint protein 1 (MDC1) and similar proteins
  17. XM_011515004.4XP_011513306.1  mediator of DNA damage checkpoint protein 1 isoform X4

    See identical proteins and their annotated locations for XP_011513306.1

    Conserved Domains (1) summary
    cd00027
    Location:17781830
    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 ...

Reference GRCh38.p14 ALT_REF_LOCI_1

Genomic

  1. NT_167244.2 Reference GRCh38.p14 ALT_REF_LOCI_1

    Range
    2029312..2046785 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 ALT_REF_LOCI_2

Genomic

  1. NT_113891.3 Reference GRCh38.p14 ALT_REF_LOCI_2

    Range
    2179547..2197021 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 ALT_REF_LOCI_3

Genomic

  1. NT_167245.2 Reference GRCh38.p14 ALT_REF_LOCI_3

    Range
    1955659..1973132 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 ALT_REF_LOCI_4

Genomic

  1. NT_167246.2 Reference GRCh38.p14 ALT_REF_LOCI_4

    Range
    2010059..2027532 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 ALT_REF_LOCI_5

Genomic

  1. NT_167247.2 Reference GRCh38.p14 ALT_REF_LOCI_5

    Range
    2043883..2061356 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 ALT_REF_LOCI_6

Genomic

  1. NT_167248.2 Reference GRCh38.p14 ALT_REF_LOCI_6

    Range
    1954920..1972393 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 ALT_REF_LOCI_7

Genomic

  1. NT_167249.2 Reference GRCh38.p14 ALT_REF_LOCI_7

    Range
    2000593..2018067 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    30564011..30581484 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)