MITF
protein-codingmelanocyte inducing transcription factor, the group of Basic helix-loop-helix proteins
Gene 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]
- WS2A
- WS2
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~228.9 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AD
Disease ID:MONDO:0007077
Submitter: G2P
Inheritance Pattern: AR
Disease ID:MONDO:0015014
Submitter: Labcorp Genetics (formerly Invitae)
Inheritance Pattern: AR
Disease ID:MONDO:0015014
Submitter: PanelApp Australia
Inheritance Pattern: AD
Disease ID:MONDO:0019517
Submitter: PanelApp Australia
Inheritance Pattern: AD
Disease ID:MONDO:0013759
Submitter: G2P
Inheritance Pattern: AD
Disease ID:MONDO:0008671
Submitter: G2P
Inheritance Pattern: AR
Disease ID:MONDO:0015014
Submitter: G2P
Inheritance Pattern: AD
Disease ID:MONDO:0013759
Submitter: Labcorp Genetics (formerly Invitae)
Inheritance Pattern: AD
Disease ID:MONDO:0019517
Submitter: ClinGen
The MITF gene has been associated with autosomal dominant Waardenburg syndrome type 2 using the ClinGen Clinical Validity Framework as of 6/14/2017. This association was made using case-level data only. At least 8 variants (missense, in-frame indel, nonsense, stoploss, frameshift, splice, and large deletion) have been reported in humans. MITF was first associated with this disease in humans as early as 1994 (Tassabehji et al.). Association is seen in at least 8 probands in 4 publications (7874167, 23512835, 27759048, 28356565). More evidence is available in the literature, but the maximum score for genetic evidence and/or experimental evidence (12 pts.) has been reached. The mechanism for disease is likely haploinsufficiency. This gene-disease association is supported by numerous animal models (Steingrimsson 1994, Hodgkinson 1998, Chen 2016), as well as biochemical functional assays (Grill 2013, Sun 2017). In summary, MITF is definitively associated with autosomal dominant Waardenburg syndrome type 2. This has been repeatedly demonstrated in both the research and clinical diagnostic settings, and has been upheld over time. This classification was approved by the ClinGen Hearing Loss Working Group on 11/21/2017.
Inheritance Pattern: AD
Disease ID:MONDO:0007077
Submitter: Ambry Genetics
Inheritance Pattern: AD
Disease ID:MONDO:0008671
Submitter: Ambry Genetics
Inheritance Pattern: AR
Disease ID:MONDO:0018094
Submitter: Ambry Genetics
Inheritance Pattern: AD
Disease ID:MONDO:0013759
Submitter: Ambry Genetics
Inheritance Pattern: AD
Disease ID:MONDO:0019518
Submitter: Orphanet
Inheritance Pattern: AD
Disease ID:MONDO:0007077
Submitter: Orphanet
Inheritance Pattern: AD
Disease ID:MONDO:0008671
Submitter: Labcorp Genetics (formerly Invitae)
Inheritance Pattern: AD
Disease ID:MONDO:0005086
Submitter: Genomics England PanelApp
Inheritance Pattern: AD
Disease ID:MONDO:0013759
Submitter: Ambry Genetics
Inheritance Pattern: AD
Disease ID:MONDO:0019517
Submitter: Orphanet
Clinical Genomic Database (CGD)
Manifestation: Audiologic/Otolaryngologic; Craniofacial; Dermatologic; Musculoskeletal; Ophthalmologic; Oncologic
Intervention: Audiologic/Otolaryngologic; Oncologic
Rationale: For Waardenburg syndrome, type 2A, Tietz albinism-deafness syndrome, and COMMAD, early recognition and treatment of hearing impairment may improve outcomes, including speech and language development; For Melanoma, cutaneous malignant, susceptibility to and Renal cell carcinoma with or without malignant melanoma, awareness may allow preventive measures, surveillance, and early diagnosis and treatment of disease
Comments: Digenic inheritance (with TYR) has been reported
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to MITF variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001354604.2. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 1 | 1 | 9 | 230 | 1 | 242 |
| missense | 9 | 24 | 616 | 26 | 1 | 676 |
| nonsense | 20 | 10 | 30 | |||
| start loss | 0 | |||||
| frameshift | 44 | 11 | 5 | 60 | ||
| splice donor/acceptor (+/-2bp) | 10 | 12 | 22 | |||
| Total | 84 | 58 | 630 | 256 | 2 | 1030 |
Highest pathogenic variant AF is 0.0027823313
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001341533.1 | 10 | MANE Select | |
| Ensembl | ENSP00000295600.8 | 10 | MANE Select | |
| RefSeq | NP_000239.1 | 9 | MANE Plus Clinical | |
| RefSeq | NP_001171896.1 | 9 | Standard |
Model Organisms & Knockout Phenotypes
Observed phenotypic effects in mouse and zebrafish models
| Gene / Model | Organism | Observed Phenotype |
|---|---|---|
| mitfa | Danio rerio | Structure: iridophore Quality: increased amount abnormal |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Melanoma - Homo sapiens (human)
- Mitophagy - animal - Homo sapiens (human)
- Pathways in cancer - Homo sapiens (human)
- Transcriptional misregulation in cancer - Homo sapiens (human)
- Osteoclast differentiation - Homo sapiens (human)
Biological Process
- negative regulation of transcription by RNA polymerase II
- transcription, DNA-templated
- regulation of transcription, DNA-templated
- positive regulation of gene expression
- osteoclast differentiation
Molecular Function
- RNA polymerase II proximal promoter sequence-specific DNA binding
- DNA-binding transcription factor activity, RNA polymerase II-specific
- DNA-binding transcription repressor activity, RNA polymerase II-specific
- DNA-binding transcription activator activity, RNA polymerase II-specific
- chromatin binding
Cellular Component
- nucleus
- nucleoplasm
- protein-containing complex
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000352241
- Coding exons
- 10
- Length
- 228903
- Individuals with no LoFs
- 125704
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 4
- Defined
- 125708
- p
- 0.0000159
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 1.47 | 243 | 317 | 0.768 | 0.0000187 | 3439 |
| Missense (PolyPhen) | 66 | 119.39 | 0.5528 | 1263 | ||
| Synonymous | 0.359 | 116 | 121 | 0.958 | 0.00000772 | 977 |
| Loss of Function | 4.38 | 4 | 29.8 | 0.134 | 0.00000191 | 289 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0 | 0.0 | absent |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.00011 | 0.00011 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.000018 | 0.000018 | rare |
| South Asian | 0 | 0.0 | absent |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Transcription factor that regulates the expression of genes with essential roles in cell differentiation, proliferation and survival. Binds to M-boxes (5'-TCATGTG-3') and symmetrical DNA sequences (E-boxes) (5'-CACGTG-3') found in the promoters of target genes, such as BCL2 and tyrosinase (TYR). Plays an important role in melanocyte development by regulating the expression of tyrosinase (TYR) and tyrosinase-related protein 1 (TYRP1). Plays a critical role in the differentiation of various cell types, such as neural crest-derived melanocytes, mast cells, osteoclasts and optic cup-derived retinal pigment epithelium. {ECO:0000269|PubMed:10587587, ECO:0000269|PubMed:22647378, ECO:0000269|PubMed:27889061, ECO:0000269|PubMed:9647758}.;
- Disease
- DISEASE: Waardenburg syndrome 2A (WS2A) [MIM:193510]: WS2 is a genetically heterogeneous, autosomal dominant disorder characterized by sensorineural deafness, pigmentary disturbances, and absence of dystopia canthorum. The frequency of deafness is higher in WS2 than in WS1. {ECO:0000269|PubMed:28236341, ECO:0000269|PubMed:8589691}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Waardenburg syndrome 2, with ocular albinism, autosomal recessive (WS2-OA) [MIM:103470]: A disorder characterized by the association of features typical of Waardenburg syndrome type 2 with ocular albinism. Patients manifest reduced visual acuity, albinotic fundus, deafness, hypomelanosis. {ECO:0000269|PubMed:9647758}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Tietz albinism-deafness syndrome (TADS) [MIM:103500]: An autosomal dominant disorder characterized by generalized hypopigmentation and congenital, bilateral, profound sensorineural deafness. {ECO:0000269|PubMed:10851256}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Melanoma, cutaneous malignant 8 (CMM8) [MIM:614456]: A malignant neoplasm of melanocytes, arising de novo or from a pre- existing benign nevus, which occurs most often in the skin but also may involve other sites. {ECO:0000269|PubMed:22012259, ECO:0000269|PubMed:22080950}. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.; DISEASE: Coloboma, osteopetrosis, microphthalmia, macrocephaly, albinism, and deafness (COMMAD) [MIM:617306]: An autosomal recessive syndrome characterized by severe microphthalmia, profound congenital sensorineural hearing loss, lack of pigment in the hair, skin, and eyes, macrocephaly, facial dysmorphism, and osteopetrosis. {ECO:0000269|PubMed:27889061}. Note=The disease is caused by mutations affecting the gene represented in this entry. An allelic combination involving at least one dominant-negative mutation, inherited in a recessive manner, represents the underlying molecular mechanism leading to COMMAD syndrome. {ECO:0000269|PubMed:27889061}.; DISEASE: Note=Variations affecting this gene are associated with susceptibility to pheochromocytomas and paragangliomas, rare neural crest-derived tumors with an approximate incidence of 1:300,000/year. {ECO:0000269|PubMed:27680874}.;
Recessive Scores
- pRec
- 0.423
Intolerance Scores
- LoFtool
- 0.203
- RVIS EVS
- -0.56
- RVIS percentile EVS
- 19.73
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.944
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |