NM_001184880.2(PCDH19):c.1640delinsTA (p.Ala547fs) AND Developmental and epileptic encephalopathy, 9

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Jun 7, 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:
RCV001247771.7

Allele description [Variation Report for NM_001184880.2(PCDH19):c.1640delinsTA (p.Ala547fs)]

NM_001184880.2(PCDH19):c.1640delinsTA (p.Ala547fs)

Gene:
PCDH19:protocadherin 19 [Gene - OMIM - HGNC]
Variant type:
Indel
Cytogenetic location:
Xq22.1
Genomic location:
Preferred name:
NM_001184880.2(PCDH19):c.1640delinsTA (p.Ala547fs)
HGVS:
  • NC_000023.11:g.100406958delinsTA
  • NG_021319.1:g.8316delinsTA
  • NM_001105243.2:c.1640delinsTA
  • NM_001184880.2:c.1640delinsTAMANE SELECT
  • NM_020766.3:c.1640delinsTA
  • NP_001098713.1:p.Ala547fs
  • NP_001171809.1:p.Ala547fs
  • NP_065817.2:p.Ala547fs
  • LRG_843t1:c.1640delinsTA
  • LRG_843:g.8316delinsTA
  • LRG_843p1:p.Ala547fs
  • NC_000023.10:g.99661956delinsTA
  • NC_000023.10:g.99661956delinsTA
  • NM_001184880.1:c.1640delinsTA
Protein change:
A547fs
Links:
dbSNP: rs1928375176
NCBI 1000 Genomes Browser:
rs1928375176
Molecular consequence:
  • NM_001105243.2:c.1640delinsTA - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001184880.2:c.1640delinsTA - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_020766.3:c.1640delinsTA - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Name:
Developmental and epileptic encephalopathy, 9 (DEE9)
Synonyms:
EPILEPSY, FEMALE-RESTRICTED, WITH MENTAL RETARDATION; JUBERG-HELLMAN SYNDROME; PCDH19-Related X-Linked Female-Limited Epilepsy with Mental Retardation; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0010246; MedGen: C1848137; Orphanet: 2076; OMIM: 300088

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001421214Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Pathogenic
(Jun 7, 2020) 		germlineclinical testing

PubMed (2)
[See all records that cite these PMIDs]

Help

Summary from all submissions

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

Citations

PubMed

Mutations and deletions in PCDH19 account for various familial or isolated epilepsies in females.

Depienne C, Trouillard O, Bouteiller D, Gourfinkel-An I, Poirier K, Rivier F, Berquin P, Nabbout R, Chaigne D, Steschenko D, Gautier A, Hoffman-Zacharska D, Lannuzel A, Lackmy-Port-Lis M, Maurey H, Dusser A, Bru M, Gilbert-Dussardier B, Roubertie A, Kaminska A, Whalen S, Mignot C, et al.

Hum Mutat. 2011 Jan;32(1):E1959-75. doi: 10.1002/humu.21373.

PubMed [citation]
PMID:
21053371
PMCID:
PMC3033517

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, SCV001421214.5

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (2)

Description

This variant has not been reported in the literature in individuals with PCDH19-related conditions. This variant is not present in population databases (ExAC no frequency). This sequence change creates a premature translational stop signal (p.Ala547Valfs*24) in the PCDH19 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in PCDH19 are known to be pathogenic (PMID: 21053371). For these reasons, this variant has been classified as Pathogenic.

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

Last Updated: Sep 29, 2024