NM_001184880.2(PCDH19):c.830_832del (p.Phe277del) AND Developmental and epileptic encephalopathy, 9

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Nov 24, 2022
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:: RCV003622678.2

Allele description [Variation Report for NM_001184880.2(PCDH19):c.830_832del (p.Phe277del)]

NM_001184880.2(PCDH19):c.830_832del (p.Phe277del)

Gene:

PCDH19:protocadherin 19 [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

Xq22.1

Genomic location:

Preferred name:

NM_001184880.2(PCDH19):c.830_832del (p.Phe277del)

HGVS:

NC_000023.11:g.100407768_100407770del
NG_021319.1:g.7506_7508del
NM_001105243.2:c.830_832del
NM_001184880.2:c.830_832delMANE SELECT
NM_020766.3:c.830_832del
NP_001098713.1:p.Phe277del
NP_001171809.1:p.Phe277del
NP_065817.2:p.Phe277del
LRG_843t1:c.830_832del
LRG_843:g.7506_7508del
LRG_843p1:p.Phe277del
NC_000023.10:g.99662764_99662766del
NC_000023.10:g.99662766_99662768del

Protein change:

F277del

Molecular consequence:

NM_001105243.2:c.830_832del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001184880.2:c.830_832del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_020766.3:c.830_832del - inframe_deletion - [Sequence Ontology: SO:0001822]

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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Rattus norvegicus kelch domain containing 10, mRNA (cDNA clone MGC:105857 IMAGE:7115168), complete cds
gi|55154096|gb|BC085351.1|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004489159	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Nov 24, 2022)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004489159

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Nov 24, 2022)

germline

clinical testing

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

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, SCV004489159.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

Description

In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. This variant has not been reported in the literature in individuals affected with PCDH19-related conditions. This variant is not present in population databases (gnomAD no frequency). This variant, c.830_832del, results in the deletion of 1 amino acid(s) of the PCDH19 protein (p.Phe277del), but otherwise preserves the integrity of the reading frame.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Sep 29, 2024

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