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NM_001354604.2(MITF):c.1182A>T (p.Glu394Asp) AND multiple conditions

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Dec 26, 2023
Review status:
1 star out of maximum of 4 stars
criteria provided, single submitter
Somatic classification
of clinical impact:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Somatic classification
of oncogenicity:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Record status:
current
Accession:
RCV003800607.2

Allele description [Variation Report for NM_001354604.2(MITF):c.1182A>T (p.Glu394Asp)]

NM_001354604.2(MITF):c.1182A>T (p.Glu394Asp)

Gene:
MITF:melanocyte inducing transcription factor [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
3p13
Genomic location:
Preferred name:
NM_001354604.2(MITF):c.1182A>T (p.Glu394Asp)
HGVS:
  • NC_000003.12:g.69964849A>T
  • NG_011631.1:g.230368A>T
  • NM_000248.4:c.861A>T
  • NM_001184967.2:c.1008A>T
  • NM_001354604.2:c.1182A>TMANE SELECT
  • NM_001354605.2:c.1179A>T
  • NM_001354606.2:c.1161A>T
  • NM_001354607.2:c.1113A>T
  • NM_001354608.2:c.1008A>T
  • NM_006722.3:c.1161A>T
  • NM_198158.3:c.843A>T
  • NM_198159.3:c.1164A>T
  • NM_198177.3:c.1116A>T
  • NM_198178.3:c.675A>T
  • NP_000239.1:p.Glu287Asp
  • NP_000239.1:p.Glu287Asp
  • NP_001171896.1:p.Glu336Asp
  • NP_001341533.1:p.Glu394Asp
  • NP_001341534.1:p.Glu393Asp
  • NP_001341535.1:p.Glu387Asp
  • NP_001341536.1:p.Glu371Asp
  • NP_001341537.1:p.Glu336Asp
  • NP_006713.1:p.Glu387Asp
  • NP_937801.1:p.Glu281Asp
  • NP_937802.1:p.Glu388Asp
  • NP_937820.1:p.Glu372Asp
  • NP_937821.2:p.Glu225Asp
  • LRG_776t1:c.861A>T
  • LRG_776:g.230368A>T
  • LRG_776p1:p.Glu287Asp
  • NC_000003.11:g.70014000A>T
  • NM_000248.3:c.861A>T
Protein change:
E225D
Molecular consequence:
  • NM_000248.4:c.861A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001184967.2:c.1008A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354604.2:c.1182A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354605.2:c.1179A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354606.2:c.1161A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354607.2:c.1113A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354608.2:c.1008A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_006722.3:c.1161A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_198158.3:c.843A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_198159.3:c.1164A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_198177.3:c.1116A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_198178.3:c.675A>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Tietz syndrome (TADS)
Synonyms:
Albinism-deafness of Tietz; Hypopigmentation/deafness of Tietz; Tietz albinism-deafness syndrome
Identifiers:
MONDO: MONDO:0007077; MedGen: C0391816; Orphanet: 42665; OMIM: 103500
Name:
Waardenburg syndrome type 2A (WS2A)
Synonyms:
WAARDENBURG SYNDROME WITHOUT DYSTOPIA CANTHORUM
Identifiers:
MONDO: MONDO:0008671; MedGen: C1860339; Orphanet: 3440; OMIM: 193510
Name:
Melanoma, cutaneous malignant, susceptibility to, 8
Synonyms:
MELANOMA AND RENAL CELL CARCINOMA, SUSCEPTIBILITY TO; Cutaneous malignant melanoma 8
Identifiers:
MONDO: MONDO:0013759; MedGen: C3152204; Orphanet: 293822; OMIM: 614456

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV004590602Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(Dec 26, 2023) 		germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV004590602.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

This sequence change replaces glutamic acid, which is acidic and polar, with aspartic acid, which is acidic and polar, at codon 287 of the MITF protein (p.Glu287Asp). This variant is present in population databases (rs137904015, gnomAD 0.003%). This variant has not been reported in the literature in individuals affected with MITF-related conditions. An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be disruptive. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Sep 29, 2024