NM_001184880.2(PCDH19):c.544G>C (p.Gly182Arg) AND Developmental and epileptic encephalopathy, 9

This record was updated by the submitter. Please see the current version.

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jul 15, 2021
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:: RCV001932562.5

Allele description

NM_001184880.2(PCDH19):c.544G>C (p.Gly182Arg)

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.544G>C (p.Gly182Arg)

HGVS:

NC_000023.11:g.100408054C>G
NG_021319.1:g.7220G>C
NM_001105243.2:c.544G>C
NM_001184880.2:c.544G>CMANE SELECT
NM_020766.3:c.544G>C
NP_001098713.1:p.Gly182Arg
NP_001171809.1:p.Gly182Arg
NP_065817.2:p.Gly182Arg
LRG_843t1:c.544G>C
LRG_843:g.7220G>C
LRG_843p1:p.Gly182Arg
NC_000023.10:g.99663052C>G

Protein change:

G182R

Links:

dbSNP: rs777840773

NCBI 1000 Genomes Browser:

rs777840773

Molecular consequence:

NM_001105243.2:c.544G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001184880.2:c.544G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_020766.3:c.544G>C - missense variant - [Sequence Ontology: SO:0001583]

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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Homo sapiens transient receptor potential cation channel subfamily C member 4 (T...
Homo sapiens transient receptor potential cation channel subfamily C member 4 (TRPC4), transcript variant epsilon, mRNA
gi|209863023|ref|NM_003306.1|

Nucleotide
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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002137365	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Jul 15, 2021)	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

SCV002137365

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Jul 15, 2021)

germline

clinical testing

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

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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 Invitae, SCV002137365.3

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

Description

This variant has not been reported in the literature in individuals affected with PCDH19-related conditions. This variant is present in population databases (rs777840773, ExAC 0.002%). This sequence change replaces glycine with arginine at codon 182 of the PCDH19 protein (p.Gly182Arg). The glycine residue is highly conserved and there is a moderate physicochemical difference between glycine and arginine. Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Class C15"). 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.

#	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: Mar 5, 2024

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