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NM_005378.6(MYCN):c.1192C>T (p.Arg398Trp) AND not provided

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
Jan 26, 2016
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:
RCV000414637.1

Allele description [Variation Report for NM_005378.6(MYCN):c.1192C>T (p.Arg398Trp)]

NM_005378.6(MYCN):c.1192C>T (p.Arg398Trp)

Gene:
MYCN:MYCN proto-oncogene, bHLH transcription factor [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
2p24.3
Genomic location:
Preferred name:
NM_005378.6(MYCN):c.1192C>T (p.Arg398Trp)
HGVS:
  • NC_000002.12:g.15945894C>T
  • NG_007457.1:g.10334C>T
  • NM_001293228.2:c.1192C>T
  • NM_001293231.2:c.559C>T
  • NM_001293233.2:c.*1127C>T
  • NM_005378.6:c.1192C>TMANE SELECT
  • NP_001280157.1:p.Arg398Trp
  • NP_001280160.1:p.Arg187Trp
  • NP_005369.2:p.Arg398Trp
  • NC_000002.11:g.16086016C>T
  • NM_005378.4:c.1192C>T
Protein change:
R187W
Links:
dbSNP: rs1057517770
NCBI 1000 Genomes Browser:
rs1057517770
Molecular consequence:
  • NM_001293233.2:c.*1127C>T - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
  • NM_001293228.2:c.1192C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001293231.2:c.559C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_005378.6:c.1192C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: CN517202

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000490644GeneDx
criteria provided, single submitter

(GeneDx Variant Classification (06012015))		Likely pathogenic
(Jan 26, 2016) 		germlineclinical testing

Citation Link

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Summary from all submissions

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

Details of each submission

From GeneDx, SCV000490644.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

The R398W variant has not been published as a pathogenic variant, nor has it been reported as abenign variant to our knowledge. The variant was not observed in approximately 6,500 individuals ofEuropean and African American ancestry in the NHLBI Exome Sequencing Project, indicating it is nota common benign variant in these populations. R398W is a non-conservative amino acid substitution,which is likely to impact secondary protein structure as these residues differ in polarity, charge, sizeand/or other properties. This substitution occurs at a position that is conserved across species, and insilico analysis predicts this variant is probably damaging to the protein structure/function. Missensevariants in nearby residues (R393C/S/H, R394H) have been reported in the Human Gene MutationDatabase in association with Feingold syndrome (Stenson et al., 2014), supporting the functionalimportance of this region of the protein. Therefore, based on the currently available information, thisvariant is likely pathogenic; however, the possibility that it is benign cannot be excluded.

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

Last Updated: Apr 23, 2022