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NM_001354604.2(MITF):c.355-1062G>C

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Interpretation:
Pathogenic/Likely pathogenic​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
3
First in ClinVar:
Dec 2, 2018
Most recent Submission:
Mar 26, 2023
Last evaluated:
Feb 28, 2023
Accession:
VCV000545639.5
Variation ID:
545639
Description:
single nucleotide variant
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NM_001354604.2(MITF):c.355-1062G>C

Allele ID
536135
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
3p13
Genomic location
3: 69936760 (GRCh38) GRCh38 UCSC
3: 69985911 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NM_001354604.2:c.355-1062G>C MANE Select
NM_000248.4:c.33+5G>C MANE Plus Clinical
NM_001184967.2:c.199-1062G>C
... more HGVS
Protein change
-
Other names
-
Canonical SPDI
NC_000003.12:69936759:G:C
Functional consequence
effect on RNA splicing [Variation Ontology VariO:0362]
Global minor allele frequency (GMAF)
-

Allele frequency
The Genome Aggregation Database (gnomAD) 0.00003
The Genome Aggregation Database (gnomAD) 0.00001
Links
dbSNP: rs1236436555
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Pathogenic 1 criteria provided, single submitter May 29, 2022 RCV002534250.1
Likely pathogenic 1 criteria provided, single submitter Feb 28, 2023 RCV003155262.1
Likely pathogenic 1 no assertion criteria provided - RCV000722130.3
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
MITF Sufficient evidence for dosage pathogenicity No evidence available GRCh38
GRCh37
493 516

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter More information
Pathogenic
(May 29, 2022)
criteria provided, single submitter
Method: clinical testing
Melanoma, cutaneous malignant, susceptibility to, 8
Waardenburg syndrome type 2A
Tietz syndrome
Affected status: unknown
Allele origin: germline
Invitae
Accession: SCV003525336.1
First in ClinVar: Feb 07, 2023
Last updated: Feb 07, 2023
Publications:
PubMed (4)
PubMed: 2137325630117279175766819536098
Comment:
This sequence change falls in intron 1 of the MITF gene. It does not directly change the encoded amino acid sequence of the MITF protein. … (more)
Likely pathogenic
(Feb 28, 2023)
criteria provided, single submitter
Method: research
Waardenburg syndrome type 2A
Affected status: yes
Allele origin: unknown
King Laboratory, University of Washington
Accession: SCV003844122.1
First in ClinVar: Mar 26, 2023
Last updated: Mar 26, 2023
Publications:
PubMed (1)
PubMed: 36633841
Comment:
This variant occurred in heterozygosity in an individual with Waardenburg syndrome including heterochromia iridis and bilateral sensorineural hearing loss of onset <18 years, in a … (more)
Likely pathogenic
(-)
no assertion criteria provided
Method: research
Waardenburg syndrome type 2
Affected status: yes
Allele origin: germline
Institute for Human Genetics, University Medical Center Freiburg
Accession: SCV000777908.1
First in ClinVar: Dec 02, 2018
Last updated: Dec 02, 2018
Comment:
Our work describes a unique depigmentation phenotype in an Argentinean boy due to a MITF mutation. Our index patient was born to consanguineous parents (siblings) … (more)
Zygosity: 1 Homozygote
Sex: male
Geographic origin: Argentina

Functional evidence

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Functional consequence Method Result Submitter Supporting information
effect on RNA splicing
  1. Method not provided
  1. Result not provided
Institute for Human Genetics, University Medical Center Freiburg
Accession: SCV000777908.1
Submitted: (May 30, 2018)
Evidence details

Citations for this variant

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Title Author Journal Year Link
Association of Genetic Diagnoses for Childhood-Onset Hearing Loss With Cochlear Implant Outcomes. Carlson RJ JAMA otolaryngology-- head & neck surgery 2023 PMID: 36633841
Homozygous intronic MITF mutation causes severe Waardenburg syndrome type 2A. Rauschendorf MA Pigment cell & melanoma research 2019 PMID: 30117279
Molecular Study of Three Lebanese and Syrian Patients with Waardenburg Syndrome and Report of Novel Mutations in the EDNRB and MITF Genes. Haddad NM Molecular syndromology 2011 PMID: 21373256
Aberrant 5' splice sites in human disease genes: mutation pattern, nucleotide structure and comparison of computational tools that predict their utilization. Buratti E Nucleic acids research 2007 PMID: 17576681
Statistical features of human exons and their flanking regions. Zhang MQ Human molecular genetics 1998 PMID: 9536098

Text-mined citations for rs1236436555...

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These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Apr 02, 2023