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NM_001184880.2(PCDH19):c.2796C>T (p.Asn932=)

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Interpretation:
Conflicting interpretations of pathogenicity​

Benign(3);Likely benign(1);Uncertain significance(2)

Review status:
criteria provided, conflicting interpretations
Submissions:
8 (Most recent: Sep 21, 2021)
Last evaluated:
Dec 7, 2020
Accession:
VCV000138601.14
Variation ID:
138601
Description:
single nucleotide variant
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NM_001184880.2(PCDH19):c.2796C>T (p.Asn932=)

Allele ID
142304
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
Xq22.1
Genomic location
X: 100341955 (GRCh38) GRCh38 UCSC
X: 99596953 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000023.10:g.99596953G>A
NC_000023.11:g.100341955G>A
NG_021319.1:g.73319C>T
... more HGVS
Protein change
-
Other names
p.N885N:AAC>AAT
Canonical SPDI
NC_000023.11:100341954:G:A
Functional consequence
-
Global minor allele frequency (GMAF)
0.00265 (A)

Allele frequency
Trans-Omics for Precision Medicine (TOPMed) 0.00262
Exome Aggregation Consortium (ExAC) 0.00271
Trans-Omics for Precision Medicine (TOPMed) 0.00241
1000 Genomes Project 0.00265
The Genome Aggregation Database (gnomAD) 0.00228
The Genome Aggregation Database (gnomAD) 0.00210
The Genome Aggregation Database (gnomAD), exomes 0.00274
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00301
Links
ClinGen: CA295141
dbSNP: rs193148631
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Benign 2 criteria provided, single submitter Dec 7, 2020 RCV000233996.8
Uncertain significance 2 criteria provided, single submitter Feb 1, 2017 RCV000416088.6
Likely benign 1 criteria provided, single submitter Jun 15, 2016 RCV000715141.1
Conflicting interpretations of pathogenicity 3 criteria provided, conflicting interpretations Nov 18, 2014 RCV000147086.5
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
PCDH19 Sufficient evidence for dosage pathogenicity No evidence available GRCh38
GRCh37
754 920

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Uncertain significance
(Oct 31, 2014)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
Genetic Services Laboratory,University of Chicago
Accession: SCV000194442.2
Submitted: (Sep 15, 2015)
Evidence details
Benign
(Dec 19, 2012)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
GeneDx
Accession: SCV000170910.12
Submitted: (Mar 26, 2018)
Evidence details
Comment:
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at … (more)
Benign
(Nov 18, 2014)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics
Accession: SCV000231001.5
Submitted: (Sep 19, 2018)
Evidence details
Other databases
http://www.egl-eurofins.com/emvc…
Benign
(Dec 07, 2020)
criteria provided, single submitter
Method: clinical testing
Early infantile epileptic encephalopathy 9
Allele origin: germline
Invitae
Accession: SCV000286297.7
Submitted: (Jan 07, 2021)
Evidence details
Likely benign
(Jun 15, 2016)
criteria provided, single submitter
Method: clinical testing
History of neurodevelopmental disorder
Allele origin: germline
Ambry Genetics
Accession: SCV000845969.3
Submitted: (Nov 30, 2020)
Evidence details
Publications
PubMed (1)
Comment:
Synonymous alterations with insufficient evidence to classify as benign
Uncertain significance
(Feb 01, 2017)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
CeGaT Praxis fuer Humangenetik Tuebingen
Accession: SCV000493317.13
Submitted: (Jul 04, 2021)
Evidence details
Likely benign
(-)
no assertion criteria provided
Method: clinical testing
Early infantile epileptic encephalopathy 9
Allele origin: germline
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Study: VKGL Data-share Consensus
Accession: SCV000734796.1
Submitted: (Apr 04, 2018)
Evidence details
Likely benign
(-)
no assertion criteria provided
Method: clinical testing
not provided
Allele origin: germline
Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center
Additional submitter:
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Study: VKGL Data-share Consensus
Accession: SCV001966543.1
Submitted: (Sep 21, 2021)
Evidence details

Functional evidence

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There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Citations for this variant

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Title Author Journal Year Link
Febrile infection-related epilepsy syndrome (FIRES) is not caused by SCN1A, POLG, PCDH19 mutations or rare copy number variations. Appenzeller S Developmental medicine and child neurology 2012 PMID: 23066759
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=PCDH19 - - - -

Text-mined citations for rs193148631...

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These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Nov 27, 2021