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    MITF melanocyte inducing transcription factor [ Homo sapiens (human) ]

    Gene ID: 4286, updated on 19-Sep-2024

    Summary

    Official Symbol
    MITFprovided by HGNC
    Official Full Name
    melanocyte inducing transcription factorprovided by HGNC
    Primary source
    HGNC:HGNC:7105
    See related
    Ensembl:ENSG00000187098 MIM:156845; AllianceGenome:HGNC:7105
    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
    MI; WS2; CMM8; WS2A; COMMAD; MITF-A; bHLHe32
    Summary
    The protein encoded by this gene is a transcription factor that contains both basic helix-loop-helix and leucine zipper structural features. The encoded protein regulates melanocyte development and is responsible for pigment cell-specific transcription of the melanogenesis enzyme genes. Heterozygous mutations in the this gene cause auditory-pigmentary syndromes, such as Waardenburg syndrome type 2 and Tietz syndrome. [provided by RefSeq, Aug 2017]
    Expression
    Broad expression in endometrium (RPKM 9.9), heart (RPKM 3.9) and 19 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See MITF in Genome Data Viewer
    Location:
    3p13
    Exon count:
    17
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (69739464..69968332)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (69776362..70005284)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (69788615..70017483)

    Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene FERM domain containing 4B Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:69534465-69535137 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr3:69560923-69561519 Neighboring gene RNA binding motif protein 43 pseudogene 1 Neighboring gene NANOG hESC enhancer GRCh37_chr3:69655392-69655947 Neighboring gene H1-8 pseudogene 1 Neighboring gene NFE2L2 motif-containing MPRA enhancer 231 Neighboring gene MITF-A promoter region Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr3:69818568-69819767 Neighboring gene RNA, 7SL, cytoplasmic 418, pseudogene Neighboring gene MITF-H promoter region Neighboring gene MITF-M distal enhancer Neighboring gene MITF-M promoter region Neighboring gene survival associated mitochondrial melanoma specific oncogenic non-coding RNA Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20055 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20056 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20057 Neighboring gene RNA binding region (RNP1, RRM) containing 3 pseudogene 1 Neighboring gene ubiquinol-cytochrome c reductase hinge protein pseudogene 4

    Genomic regions, transcripts, and products

    Expression

    • 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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    Associated conditions

    Description Tests
    Coloboma, osteopetrosis, microphthalmia, macrocephaly, albinism, and deafness
    MedGen: C4310625 OMIM: 617306 GeneReviews: Not available
    Compare labs
    Melanoma, cutaneous malignant, susceptibility to, 8
    MedGen: C3152204 OMIM: 614456 GeneReviews: Not available
    Compare labs
    Tietz syndrome
    MedGen: C0391816 OMIM: 103500 GeneReviews: Not available
    Compare labs
    Waardenburg syndrome type 2A
    MedGen: C1860339 OMIM: 193510 GeneReviews: Not available
    Compare labs

    Copy number response

    Description
    Copy number response
    Triplosensitivity

    No evidence available (Last evaluated 2021-04-13)

    ClinGen Genome Curation Page
    Haploinsufficency

    Sufficient evidence for dosage pathogenicity (Last evaluated 2021-04-13)

    ClinGen Genome Curation PagePubMed

    EBI GWAS Catalog

    Description
    Genome wide association study (GWAS) of Chagas cardiomyopathy in Trypanosoma cruzi seropositive subjects.
    EBI GWAS Catalog

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Gene Ontology Provided by GOA

    Process Evidence Code Pubs
    involved_in Wnt signaling pathway IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in bone remodeling IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in camera-type eye development IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in cell fate commitment IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in melanocyte apoptotic process IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in melanocyte differentiation IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in melanocyte differentiation NAS
    Non-traceable Author Statement
    more info
    PubMed 
    involved_in negative regulation of apoptotic process IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in negative regulation of cell migration IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in negative regulation of transcription by RNA polymerase II IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in osteoclast differentiation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in positive regulation of DNA-templated transcription IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of DNA-templated transcription NAS
    Non-traceable Author Statement
    more info
    PubMed 
    involved_in positive regulation of DNA-templated transcription initiation IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of gene expression IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of gene expression IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of transcription by RNA polymerase II IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of transcription by RNA polymerase II IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in protein-containing complex assembly IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in regulation of DNA-templated transcription IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in regulation of DNA-templated transcription NAS
    Non-traceable Author Statement
    more info
    PubMed 
    involved_in regulation of RNA biosynthetic process IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in regulation of cell population proliferation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in regulation of osteoclast differentiation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    Component Evidence Code Pubs
    located_in chromatin ISA
    Inferred from Sequence Alignment
    more info
     
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in cytosol TAS
    Traceable Author Statement
    more info
     
    located_in lysosomal membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
     
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    is_active_in nucleus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in nucleus NAS
    Non-traceable Author Statement
    more info
    PubMed 
    part_of protein-containing complex IDA
    Inferred from Direct Assay
    more info
    PubMed 

    General protein information

    Preferred Names
    microphthalmia-associated transcription factor
    Names
    class E basic helix-loop-helix protein 32
    melanogenesis associated transcription factor
    microphtalmia-associated transcription factor

    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_011631.1 RefSeqGene

      Range
      4954..233856
      Download
      GenBank, FASTA, Sequence Viewer (Graphics), LRG_776

    mRNA and Protein(s)

    1. NM_000248.4NP_000239.1  microphthalmia-associated transcription factor isoform 4

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) differs in the 5' UTR, the 5' coding region and uses an alternate, in-frame splice site in the 3' coding region, compared to variant 1. The resulting isoform (4), also known as isoform MITF-M, has a distinct N-terminus and is shorter than isoform 1.
      Source sequence(s)
      AC104449, AL117653, AW242257, BQ219650, Z29678
      Consensus CDS
      CCDS2913.1
      UniProtKB/TrEMBL
      A0A0H3W5T2
      Related
      ENSP00000377880.3, ENST00000394351.9
      Conserved Domains (3) summary
      cd00083
      Location:202262
      HLH; Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long. A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, ...
      pfam11851
      Location:290403
      DUF3371; Domain of unknown function (DUF3371)
      pfam15951
      Location:1187
      MITF_TFEB_C_3_N; MITF/TFEB/TFEC/TFE3 N-terminus
    2. NM_001184967.2NP_001171896.1  microphthalmia-associated transcription factor isoform 7

      Status: REVIEWED

      Description
      Transcript Variant: This variant (7) differs in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at a downstream start codon, compared to variant 1. The encoded isoform (7) is shorter than isoform 1.
      Source sequence(s)
      AC104445, AC104449, AK296129, AL110195, AL117653, AW242257
      Consensus CDS
      CCDS54607.1
      UniProtKB/TrEMBL
      A0A0H3W5T2
      Related
      ENSP00000418845.1, ENST00000472437.5
      Conserved Domains (3) summary
      cd00083
      Location:251311
      HLH; Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long. A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, ...
      pfam11851
      Location:339458
      DUF3371; Domain of unknown function (DUF3371)
      pfam15951
      Location:4142
      MITF_TFEB_C_3_N; MITF/TFEB/TFEC/TFE3 N-terminus
    3. NM_001184968.2NP_001171897.1  microphthalmia-associated transcription factor isoform 8

      Status: REVIEWED

      Description
      Transcript Variant: This variant (8) has multiple differences, compared to variant 1. These differences result in a distinct 5' UTR and cause translation initiation at an alternate start codon, compared to variant 1. The encoded protein (isoform 8) is shorter than isoform 1 and has unique N- and C-termini.
      Source sequence(s)
      AC104449, BC012503, BQ219650
      Consensus CDS
      CCDS74962.1
      UniProtKB/TrEMBL
      A0A087WXU1, E9PKJ8
      Related
      ENSP00000481286.1, ENST00000394348.2
      Conserved Domains (1) summary
      pfam15951
      Location:1188
      MITF_TFEB_C_3_N; MITF/TFEB/TFEC/TFE3 N-terminus
    4. NM_001354604.2NP_001341533.1  microphthalmia-associated transcription factor isoform 9

      Status: REVIEWED

      Source sequence(s)
      AC099326, AC104445, AC104449
      Consensus CDS
      CCDS87108.1
      UniProtKB/Swiss-Prot
      B4DJL2, D3K197, E9PFN0, O75030, Q14841, Q9P2V0, Q9P2V1, Q9P2V2, Q9P2Y8
      UniProtKB/TrEMBL
      A8K5K3
      Related
      ENSP00000295600.8, ENST00000352241.9
      Conserved Domains (3) summary
      cd00083
      Location:309369
      HLH; Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long. A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, ...
      pfam11851
      Location:397516
      DUF3371; Domain of unknown function (DUF3371)
      pfam15951
      Location:56194
      MITF_TFEB_C_3_N; MITF/TFEB/TFEC/TFE3 N-terminus
    5. NM_001354605.2NP_001341534.1  microphthalmia-associated transcription factor isoform 10

      Status: REVIEWED

      Source sequence(s)
      AC099326, AC104445, AC104449
      UniProtKB/TrEMBL
      A8K5K3
      Conserved Domains (3) summary
      cd00083
      Location:308368
      HLH; Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long. A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, ...
      pfam11851
      Location:396515
      DUF3371; Domain of unknown function (DUF3371)
      pfam15951
      Location:55193
      MITF_TFEB_C_3_N; MITF/TFEB/TFEC/TFE3 N-terminus
    6. NM_001354606.2NP_001341535.1  microphthalmia-associated transcription factor isoform 11

      Status: REVIEWED

      Source sequence(s)
      AC099326, AC104445, AC104449
      UniProtKB/TrEMBL
      A8K5K3
      Conserved Domains (1) summary
      cd18926
      Location:293396
      bHLHzip_MITF; basic Helix-Loop-Helix-zipper (bHLHzip) domain found in microphthalmia-associated transcription factor (MITF) and similar proteins
    7. NM_001354607.2NP_001341536.1  microphthalmia-associated transcription factor isoform 12

      Status: REVIEWED

      Source sequence(s)
      AC099326, AC104445, AC104449, AC124915
      Consensus CDS
      CCDS93308.1
      UniProtKB/TrEMBL
      A0A8I5KSZ4, B4DNC7
      Related
      ENSP00000510225.1, ENST00000687384.1
      Conserved Domains (3) summary
      cd00083
      Location:286346
      HLH; Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long. A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, ...
      pfam11851
      Location:374493
      DUF3371; Domain of unknown function (DUF3371)
      pfam15951
      Location:39177
      MITF_TFEB_C_3_N; MITF/TFEB/TFEC/TFE3 N-terminus
    8. NM_001354608.2NP_001341537.1  microphthalmia-associated transcription factor isoform 7

      Status: REVIEWED

      Description
      Transcript Variant: This variant (13), as well as variant 7, encodes isoform 7.
      Source sequence(s)
      AC099326, AC104445, AC104449, AC124915
      Consensus CDS
      CCDS54607.1
      UniProtKB/TrEMBL
      A0A0H3W5T2
      Conserved Domains (3) summary
      cd00083
      Location:251311
      HLH; Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long. A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, ...
      pfam11851
      Location:339458
      DUF3371; Domain of unknown function (DUF3371)
      pfam15951
      Location:4142
      MITF_TFEB_C_3_N; MITF/TFEB/TFEC/TFE3 N-terminus
    9. NM_006722.3NP_006713.1  microphthalmia-associated transcription factor isoform 3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR and the 5' coding region, compared to variant 1. The resulting isoform (3), also known as isoform MITF-C, has a distinct N-terminus and is shorter than isoform 1.
      Source sequence(s)
      AB006988, AC104449, AL110195, AL117653, AW242257
      UniProtKB/TrEMBL
      B4DNC7
      Related
      ENSP00000391803.3, ENST00000448226.9
      Conserved Domains (3) summary
      cd00083
      Location:302362
      HLH; Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long. A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, ...
      pfam11851
      Location:390503
      DUF3371; Domain of unknown function (DUF3371)
      pfam15951
      Location:55193
      MITF_TFEB_C_3_N; MITF/TFEB/TFEC/TFE3 N-terminus
    10. NM_198158.3NP_937801.1  microphthalmia-associated transcription factor isoform 5

      Status: REVIEWED

      Description
      Transcript Variant: This variant (5) differs in the 5' UTR and the 5' coding region, compared to variant 1. The resulting isoform (5), has a distinct N-terminus and is shorter than isoform 1.
      Source sequence(s)
      AC104449, AL117653, AW242257, BC026961, BQ219650
      Consensus CDS
      CCDS43107.1
      UniProtKB/TrEMBL
      A0A0H3W5T2
      Related
      ENSP00000324246.6, ENST00000314557.10
      Conserved Domains (3) summary
      cd00083
      Location:196256
      HLH; Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long. A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, ...
      pfam11851
      Location:284403
      DUF3371; Domain of unknown function (DUF3371)
      pfam15951
      Location:1187
      MITF_TFEB_C_3_N; MITF/TFEB/TFEC/TFE3 N-terminus
    11. NM_198159.3NP_937802.1  microphthalmia-associated transcription factor isoform 1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript, and encodes the longest isoform (1), also known as isoform MITF-A.
      Source sequence(s)
      AC104449, AL110195, AL117653, AW242257, DA058963
      Consensus CDS
      CCDS43106.1
      UniProtKB/TrEMBL
      A8K5K3
      Related
      ENSP00000494105.1, ENST00000642352.1
      Conserved Domains (3) summary
      cd00083
      Location:303363
      HLH; Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long. A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, ...
      pfam11851
      Location:391504
      DUF3371; Domain of unknown function (DUF3371)
      pfam15951
      Location:56194
      MITF_TFEB_C_3_N; MITF/TFEB/TFEC/TFE3 N-terminus
    12. NM_198177.3NP_937820.1  microphthalmia-associated transcription factor isoform 2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR and the 5' coding region, compared to variant 1. The resulting isoform (2), also known as isoform MITF-H, has a distinct N-terminus and is shorter than isoform 1.
      Source sequence(s)
      AC104449, AK297858, AL110195, AL117653, AW242257, DC388606
      Consensus CDS
      CCDS46865.1
      UniProtKB/TrEMBL
      B4DNC7
      Related
      ENSP00000324443.5, ENST00000314589.11
      Conserved Domains (3) summary
      cd00083
      Location:287347
      HLH; Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long. A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, ...
      pfam11851
      Location:375488
      DUF3371; Domain of unknown function (DUF3371)
      pfam15951
      Location:40178
      MITF_TFEB_C_3_N; MITF/TFEB/TFEC/TFE3 N-terminus
    13. NM_198178.3NP_937821.2  microphthalmia-associated transcription factor isoform 6

      Status: REVIEWED

      Description
      Transcript Variant: This variant (6) differs in the 5' UTR and the 5' coding region, and uses two alternate, in-frame splice sites in the coding region compared to variant 1. The resulting isoform (6), also known as isoform MITF-Mdel, has a distinct N-terminus and is shorter than isoform 1.
      Source sequence(s)
      AC104449, AL117653, AW242257, BQ219650, GU355676
      Consensus CDS
      CCDS46866.2
      UniProtKB/TrEMBL
      A0A0H3W5T2
      Related
      ENSP00000435909.1, ENST00000531774.1
      Conserved Domains (3) summary
      cd00083
      Location:140200
      HLH; Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long. A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, ...
      pfam11851
      Location:228341
      DUF3371; Domain of unknown function (DUF3371)
      pfam15951
      Location:1131
      MITF_TFEB_C_3_N; MITF/TFEB/TFEC/TFE3 N-terminus

    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

    1. NC_000003.12 Reference GRCh38.p14 Primary Assembly

      Range
      69739464..69968332
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060927.1 Alternate T2T-CHM13v2.0

      Range
      69776362..70005284
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)