MITF

protein-coding

melanocyte 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]

Previous symbols:
  • WS2A
  • WS2

MANE transcript

NM_001354604.2

Inheritance

AD, AR

ClinVar variants

P:142U:630B:258

Top phenotype

Waardenburg syndrome, type 2A; Tietz albinism-deafness syndrome; Coloboma, osteopetrosis, microphthalmia, macrocephaly, albinism, and deafness (COMMAD); Melanoma, cutaneous malignant, susceptibility to, 8; Renal cell carcinoma with or without malignant melanoma

gnomAD constraint

pLI —, LoF o/e 0.13

Max pathogenic AF

—

Genomic locus

chr3:69,739,456-69,968,336

External References & Databases

Transcript & Mutation Effects

hg38 • Region Span ~228.9 kb
Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

Tietz syndromeDEFINITIVE

Inheritance Pattern: AD

Disease ID:MONDO:0007077

Submitter: G2P

coloboma, osteopetrosis, microphthalmia, macrocephaly, albinism, and deafnessSTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0015014

Submitter: Labcorp Genetics (formerly Invitae)

coloboma, osteopetrosis, microphthalmia, macrocephaly, albinism, and deafnessSTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0015014

Submitter: PanelApp Australia

Waardenburg syndrome type 2STRONG

Inheritance Pattern: AD

Disease ID:MONDO:0019517

Submitter: PanelApp Australia

melanoma, cutaneous malignant, susceptibility to, 8LIMITED

Inheritance Pattern: AD

Disease ID:MONDO:0013759

Submitter: G2P

Waardenburg syndrome type 2ADEFINITIVE

Inheritance Pattern: AD

Disease ID:MONDO:0008671

Submitter: G2P

coloboma, osteopetrosis, microphthalmia, macrocephaly, albinism, and deafnessSTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0015014

Submitter: G2P

melanoma, cutaneous malignant, susceptibility to, 8STRONG

Inheritance Pattern: AD

Disease ID:MONDO:0013759

Submitter: Labcorp Genetics (formerly Invitae)

Waardenburg syndrome type 2DEFINITIVE

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.

Tietz syndromeMODERATE

Inheritance Pattern: AD

Disease ID:MONDO:0007077

Submitter: Ambry Genetics

Waardenburg syndrome type 2ADEFINITIVE

Inheritance Pattern: AD

Disease ID:MONDO:0008671

Submitter: Ambry Genetics

Waardenburg syndromeMODERATE

Inheritance Pattern: AR

Disease ID:MONDO:0018094

Submitter: Ambry Genetics

melanoma, cutaneous malignant, susceptibility to, 8MODERATE

Inheritance Pattern: AD

Disease ID:MONDO:0013759

Submitter: Ambry Genetics

Waardenburg-Shah syndromeSUPPORTIVE

Inheritance Pattern: AD

Disease ID:MONDO:0019518

Submitter: Orphanet

Tietz syndromeSUPPORTIVE

Inheritance Pattern: AD

Disease ID:MONDO:0007077

Submitter: Orphanet

Waardenburg syndrome type 2ASTRONG

Inheritance Pattern: AD

Disease ID:MONDO:0008671

Submitter: Labcorp Genetics (formerly Invitae)

renal cell carcinomaMODERATE

Inheritance Pattern: AD

Disease ID:MONDO:0005086

Submitter: Genomics England PanelApp

melanoma, cutaneous malignant, susceptibility to, 8MODERATE

Inheritance Pattern: AD

Disease ID:MONDO:0013759

Submitter: Ambry Genetics

Waardenburg syndrome type 2SUPPORTIVE

Inheritance Pattern: AD

Disease ID:MONDO:0019517

Submitter: Orphanet

Clinical Genomic Database (CGD)

Waardenburg syndrome, type 2A; Tietz albinism-deafness syndrome; Coloboma, osteopetrosis, microphthalmia, macrocephaly, albinism, and deafness (COMMAD); Melanoma, cutaneous malignant, susceptibility to, 8; Renal cell carcinoma with or without malignant melanomaAD

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

Refs: 13985019; 5006208; 331943; 666627; 7951321; 7874167; 7702105; 7573125; 8589691; 9158138; 10851256; 18510545; 20024939; 22012259; 22080950; 23167872; 23414473; 23774529; 23802662; 24638154; 24767713; 27889061Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to MITF variants in ClinVar

29 Conditions Cataloged
Waardenburg syndrome type 2ATotal: 906
Tietz syndromeTotal: 841
Melanoma, cutaneous malignant, susceptibility to, 8Total: 836
Hereditary cancer-predisposing syndromeTotal: 536
not providedTotal: 290
MITF-related disorderTotal: 81
not specifiedTotal: 58
Coloboma, osteopetrosis, microphthalmia, macrocephaly, albinism, and deafnessTotal: 37

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.

EffectPLPVUSLBBSum
synonymous
1
clinvar
1
clinvar
9
clinvar
230
clinvar
1
clinvar
242
missense
9
clinvar
24
clinvar
616
clinvar
26
clinvar
1
clinvar
676
nonsense
20
clinvar
10
clinvar
30
start loss
0
frameshift
44
clinvar
11
clinvar
5
clinvar
60
splice donor/acceptor (+/-2bp)
10
clinvar
12
clinvar
22
Total845863025621030

Highest pathogenic variant AF is 0.0027823313

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 72 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_001354604.2RefSeqNP_001341533.110MANE Select
ENST00000352241.9EnsemblENSP00000295600.810MANE Select
NM_000248.4RefSeqNP_000239.19MANE Plus Clinical
NM_001184967.2RefSeqNP_001171896.19Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / ModelOrganismObserved Phenotype
mitfaDanio 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: gnomAD

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-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense1.472433170.7680.00001873439
Missense (PolyPhen)66119.390.55281263
Synonymous0.3591161210.9580.00000772977
Loss of Function4.38429.80.1340.00000191289

Population LoF Frequency

PopulationCAFp-valueStatus
African00.0absent
Latino/Admixed American00.0absent
Ashkenazi Jewish00.0absent
East Asian0.000110.00011rare
Finnish00.0absent
European (Non-Finnish)0.0000180.000018rare
South Asian00.0absent
Other00.0absent

dbNSFP Gene Annotations

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
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