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NM_001365536.1(SCN9A):c.1326G>A (p.Ala442=)

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Interpretation:
Conflicting interpretations of pathogenicity​

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

Review status:
criteria provided, conflicting interpretations
Submissions:
4 (Most recent: Sep 23, 2021)
Last evaluated:
Nov 24, 2020
Accession:
VCV000193860.5
Variation ID:
193860
Description:
single nucleotide variant
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NM_001365536.1(SCN9A):c.1326G>A (p.Ala442=)

Allele ID
191023
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
2q24.3
Genomic location
2: 166286612 (GRCh38) GRCh38 UCSC
2: 167143122 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
LRG_369:g.94376G>A
LRG_369t1:c.1326G>A LRG_369p1:p.Ala442=
NC_000002.11:g.167143122C>T
... more HGVS
Protein change
-
Other names
-
Canonical SPDI
NC_000002.12:166286611:C:T
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00084
The Genome Aggregation Database (gnomAD) 0.00111
Exome Aggregation Consortium (ExAC) 0.00054
The Genome Aggregation Database (gnomAD), exomes 0.00024
Trans-Omics for Precision Medicine (TOPMed) 0.00105
Links
ClinGen: CA239541
dbSNP: rs200065104
Varsome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Likely benign 1 criteria provided, single submitter - RCV000242152.5
Benign 1 criteria provided, single submitter Nov 24, 2020 RCV001084151.2
Conflicting interpretations of pathogenicity 2 criteria provided, conflicting interpretations Mar 20, 2020 RCV000724887.4
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
SCN1A-AS1 - - - GRCh38 - 1165
SCN9A - - GRCh38
GRCh37
235 1427

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Likely benign
(-)
criteria provided, single submitter
Method: clinical testing
NOT SPECIFIED
Allele origin: germline
PreventionGenetics,PreventionGenetics
Accession: SCV000309300.1
Submitted: (Apr 28, 2016)
Evidence details
Uncertain significance
(Jun 02, 2015)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics
Accession: SCV000225306.5
Submitted: (Sep 19, 2018)
Evidence details
Other databases
http://www.egl-eurofins.com/emvc…
Benign
(Nov 24, 2020)
criteria provided, single submitter
Method: clinical testing
Hereditary sensory and autonomic neuropathy type IIA
Generalized epilepsy with febrile seizures plus, type 7
Allele origin: germline
Invitae
Accession: SCV000559257.6
Submitted: (Jan 07, 2021)
Evidence details
Likely benign
(Mar 20, 2020)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV000727645.2
Submitted: (Sep 23, 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
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=SCN9A - - - -

Text-mined citations for rs200065104...

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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 Sep 25, 2021