NM_001184880.2(PCDH19):c.593G>T (p.Arg198Leu) AND not provided

Clinical significance:Pathogenic/Likely pathogenic (Last evaluated: Aug 1, 2020)

Review status:2 stars out of maximum of 4 stars

criteria provided, multiple submitters, no conflicts

Based on:
2 submissions [Details]
Record status:
current
Accession:
RCV000519539.2

Allele description [Variation Report for NM_001184880.2(PCDH19):c.593G>T (p.Arg198Leu)]

NM_001184880.2(PCDH19):c.593G>T (p.Arg198Leu)

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.593G>T (p.Arg198Leu)
HGVS:
  • NC_000023.11:g.100408005C>A
  • NG_021319.1:g.7269G>T
  • NM_001105243.2:c.593G>T
  • NM_001184880.2:c.593G>TMANE SELECT
  • NM_020766.3:c.593G>T
  • NP_001098713.1:p.Arg198Leu
  • NP_001171809.1:p.Arg198Leu
  • NP_065817.2:p.Arg198Leu
  • LRG_843t1:c.593G>T
  • LRG_843:g.7269G>T
  • LRG_843p1:p.Arg198Leu
  • NC_000023.10:g.99663003C>A
  • NM_001184880.1:c.593G>T
Protein change:
R198L
Links:
dbSNP: rs772837341
NCBI 1000 Genomes Browser:
rs772837341
Molecular consequence:
  • NM_001105243.2:c.593G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001184880.2:c.593G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_020766.3:c.593G>T - missense variant - [Sequence Ontology: SO:0001583]
Observations:
1

Condition(s)

Identifiers:
MedGen: CN517202

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000617394GeneDxcriteria provided, single submitter
Likely pathogenic
(Oct 6, 2017)
germlineclinical testing

Citation Link,

SCV001501131CeGaT Praxis fuer Humangenetik Tuebingencriteria provided, single submitter
Pathogenic
(Aug 1, 2020)
germlineclinical testing

Citation Link

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyes1not providednot providednot providednot providedclinical testing

Details of each submission

From GeneDx, SCV000617394.2

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

Description

The R198L variant in the PCDH19 gene has been reported previously in a female with early-onset seizures and autistic features (Higurashi et al., 2013). The R198L variant is not observed in large population cohorts (Lek et al., 2016). The R198L variant is a non-conservative amino acid substitution, which is likely to impact secondary protein structure as these residues differ in polarity, charge, size and/or other properties. This substitution occurs at a position that is conserved across species. In silico analysis predicts this variant is probably damaging to the protein structure/function. Therefore, this variant 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

From CeGaT Praxis fuer Humangenetik Tuebingen, SCV001501131.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot provided1not providednot providednot provided

Last Updated: Jul 10, 2021

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