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NM_001184880.2(PCDH19):c.1330A>G (p.Thr444Ala) AND not provided

Germline classification:
Likely benign (2 submissions)
Last evaluated:
Jun 25, 2020
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:
RCV001355177.4

Allele description [Variation Report for NM_001184880.2(PCDH19):c.1330A>G (p.Thr444Ala)]

NM_001184880.2(PCDH19):c.1330A>G (p.Thr444Ala)

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.1330A>G (p.Thr444Ala)
Other names:
p.T444A:ACT>GCT
HGVS:
  • NC_000023.11:g.100407268T>C
  • NG_021319.1:g.8006A>G
  • NM_001105243.2:c.1330A>G
  • NM_001184880.2:c.1330A>GMANE SELECT
  • NM_020766.3:c.1330A>G
  • NP_001098713.1:p.Thr444Ala
  • NP_001171809.1:p.Thr444Ala
  • NP_065817.2:p.Thr444Ala
  • LRG_843t1:c.1330A>G
  • LRG_843:g.8006A>G
  • LRG_843p1:p.Thr444Ala
  • NC_000023.10:g.99662266T>C
  • NM_001105243.1:c.1330A>G
  • NM_001184880.1:c.1330A>G
Protein change:
T444A
Links:
dbSNP: rs201671718
NCBI 1000 Genomes Browser:
rs201671718
Molecular consequence:
  • NM_001105243.2:c.1330A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001184880.2:c.1330A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_020766.3:c.1330A>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000241943GeneDx
criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)
Likely benign
(Jun 25, 2020)
germlineclinical testing

Citation Link,

SCV001549980Department of Pathology and Laboratory Medicine, Sinai Health System - The Canadian Open Genetics Repository (COGR)

See additional submitters

no assertion criteria provided
Uncertain significanceunknownclinical testing

Summary from all submissions

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

Details of each submission

From GeneDx, SCV000241943.9

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

From Department of Pathology and Laboratory Medicine, Sinai Health System - The Canadian Open Genetics Repository (COGR), SCV001549980.1

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

Description

The PCDH19 p.Thr444Ala variant was not identified in the literature nor was it identified in Cosmic or LOVD 3.0. The variant was identified in dbSNP (ID: rs201671718) and in ClinVar (classified as likely benign by GeneDx and Uncertain significance by Genetic Services Laboratory, University of Chicago). The variant was also identified in control databases in 26 of 203692 chromosomes (8 hemizygous) at a frequency of 0.000128 (Genome Aggregation Database Feb 27, 2017). The variant was observed in the following populations: European (non-Finnish) in 25 of 92285 chromosomes (freq: 0.0002709) and Other in 1 of 5270 chromosome (freq: 0.0001898), but not in the African, Latino, Ashkenazi Jewish, East Asian, European (Finnish), and South Asian populations. The variant occurs outside of the splicing consensus sequence and in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer) do not predict a difference in splicing. The p.Thr444 residue is conserved across mammals and other organisms, and four out of five computational analyses (PolyPhen-2, SIFT, AlignGVGD, BLOSUM, MutationTaster) suggest that the variant may impact the protein; however, this information is not predictive enough to assume pathogenicity. In summary, based on the above information the clinical significance of this variant cannot be determined with certainty at this time. This variant is classified as a variant of uncertain significance.

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

Last Updated: Sep 29, 2024