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NM_004519.4(KCNQ3):c.1564G>A (p.Val522Ile)

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Interpretation:
Conflicting interpretations of pathogenicity​

Likely benign(2);Uncertain significance(2)

Review status:
criteria provided, conflicting interpretations
Submissions:
4 (Most recent: Mar 28, 2019)
Last evaluated:
Nov 8, 2018
Accession:
VCV000193878.2
Variation ID:
193878
Description:
single nucleotide variant
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NM_004519.4(KCNQ3):c.1564G>A (p.Val522Ile)

Allele ID
191041
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
8q24.22
Genomic location
8: 132140080 (GRCh38) GRCh38 UCSC
8: 133152327 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000008.10:g.133152327C>T
NC_000008.11:g.132140080C>T
NM_001204824.1:c.1204G>A NP_001191753.1:p.Val402Ile missense
... more HGVS
Protein change
V522I
Other names
-
Functional consequence
-
Global minor allele frequency (GMAF)
0.00020 (T)

Allele frequency
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00015
1000 Genomes Project 0.00020
Trans-Omics for Precision Medicine (TOPMed) 0.00003
Exome Aggregation Consortium (ExAC) 0.00007
The Genome Aggregation Database (gnomAD), exomes 0.00008
Links
dbSNP: rs143683496
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Uncertain significance 1 criteria provided, single submitter Dec 22, 2015 RCV000174103.2
Likely benign 1 criteria provided, single submitter Jun 14, 2016 RCV000300549.1
Conflicting interpretations of pathogenicity 2 criteria provided, conflicting interpretations Nov 8, 2018 RCV000404166.3
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
KCNQ3 - - GRCh38
GRCh37
460 511

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Likely benign
(Jun 14, 2016)
criteria provided, single submitter
Method: clinical testing
Benign Familial Neonatal Seizures
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000471919.2
Submitted: (Oct 18, 2016)
Evidence details
Likely benign
(Jun 14, 2016)
criteria provided, single submitter
Method: clinical testing
Benign Neonatal Epilepsy
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000471920.2
Submitted: (Oct 18, 2016)
Evidence details
Uncertain significance
(Dec 22, 2015)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
EGL Genetic Diagnostics,Eurofins Clinical Diagnostics
Accession: SCV000225343.5
Submitted: (Sep 19, 2018)
Evidence details
Other databases
http://www.egl-eurofins.com/em...
Uncertain significance
(Nov 08, 2018)
criteria provided, single submitter
Method: clinical testing
Benign familial neonatal seizures
Allele origin: germline
Invitae
Accession: SCV000769695.3
Submitted: (Mar 28, 2019)
Evidence details
Publications
PubMed (1)
Comment:
This sequence change replaces valine with isoleucine at codon 522 of the KCNQ3 protein (p.Val522Ile). The valine residue is moderately conserved and there is a ... (more)

Citations for this variant

Title Author Journal Year Link
Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria. Nykamp K Genetics in medicine : official journal of the American College of Medical Genetics 2017 PMID: 28492532
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=KCNQ3 - - - -

Record last updated Aug 30, 2019