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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
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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

    See identical proteins and their annotated locations for NP_000239.1

    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

    See identical proteins and their annotated locations for NP_001171897.1

    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

    See identical proteins and their annotated locations for NP_006713.1

    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

    See identical proteins and their annotated locations for NP_937801.1

    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

    See identical proteins and their annotated locations for NP_937802.1

    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

    See identical proteins and their annotated locations for NP_937820.1

    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

    See identical proteins and their annotated locations for NP_937821.2

    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)