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NM_001184880.2(PCDH19):c.1384G>A (p.Val462Met) AND not specified

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Jun 13, 2017
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:
RCV000498791.1

Allele description

NM_001184880.2(PCDH19):c.1384G>A (p.Val462Met)

Gene:
PCDH19:protocadherin 19 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
Xq22.1
Genomic location:
Preferred name:
NM_001184880.2(PCDH19):c.1384G>A (p.Val462Met)
HGVS:
  • NC_000023.11:g.100407214C>T
  • NG_021319.1:g.8060G>A
  • NM_001105243.2:c.1384G>A
  • NM_001184880.2:c.1384G>AMANE SELECT
  • NM_020766.3:c.1384G>A
  • NP_001098713.1:p.Val462Met
  • NP_001171809.1:p.Val462Met
  • NP_065817.2:p.Val462Met
  • LRG_843t1:c.1384G>A
  • LRG_843:g.8060G>A
  • LRG_843p1:p.Val462Met
  • NC_000023.10:g.99662212C>T
  • NM_001184880.1:c.1384G>A
Protein change:
V462M
Links:
dbSNP: rs200637767
NCBI 1000 Genomes Browser:
rs200637767
Molecular consequence:
  • NM_001105243.2:c.1384G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001184880.2:c.1384G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_020766.3:c.1384G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:
AllHighlyPenetrant
Identifiers:
MedGen: CN169374

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000590364GeneDx
criteria provided, single submitter

(GeneDx Variant Classification (06012015))		Uncertain significance
(Jun 13, 2017) 		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, SCV000590364.2

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

Description

A variant of uncertain significance has been identified in the PCDH19 gene. The V462M variant has not been published as a pathogenic variant, nor has it been reported as a benign variant to our knowledge. The V462M variant is observed in 5/47989 (0.01%) alleles from individuals of European background; including an individual who is hemizygous for the V462M variant (Lek et al., 2016; 1000 Genomes Consortium et al., 2015; Exome Variant Server). This substitution occurs at a position that is conserved across species. However, the V462M variant is a conservative amino acid substitution, which is not likely to impact secondary protein structure as these residues share similar properties. In silico analysis is inconsistent in its predictions as to whether or not the variant is damaging to the protein structure/function. Therefore, based on the currently available information, it is unclear whether this variant is a pathogenic variant or a rare benign variant.

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

Last Updated: Feb 27, 2021