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NM_001365536.1(SCN9A):c.2720G>A (p.Arg907Gln)

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Interpretation:
Likely pathogenic​

Review status:
criteria provided, single submitter
Submissions:
2 (Most recent: Jun 30, 2021)
Last evaluated:
Aug 4, 2019
Accession:
VCV000938920.3
Variation ID:
938920
Description:
single nucleotide variant
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NM_001365536.1(SCN9A):c.2720G>A (p.Arg907Gln)

Allele ID
930962
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
2q24.3
Genomic location
2: 166277137 (GRCh38) GRCh38 UCSC
2: 167133647 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000002.12:g.166277137C>T
NC_000002.11:g.167133647C>T
NM_001365536.1:c.2720G>A MANE Select NP_001352465.1:p.Arg907Gln missense
... more HGVS
Protein change
R907Q, R896Q
Other names
-
Canonical SPDI
NC_000002.12:166277136:C:T
Functional consequence
loss_of_function_variant [Sequence Ontology SO:0002054]
Global minor allele frequency (GMAF)
-

Allele frequency
-
Links
dbSNP: rs1024152367
Varsome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Likely pathogenic 1 criteria provided, single submitter Aug 4, 2019 RCV001208223.2
Pathogenic 1 no assertion criteria provided - RCV001528173.1
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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 - 1164
SCN9A - - GRCh38
GRCh37
235 1426

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Likely pathogenic
(Aug 04, 2019)
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: SCV001379600.2
Submitted: (Jan 07, 2021)
Evidence details
Publications
PubMed (2)
Comment:
This sequence change replaces arginine with glutamine at codon 896 of the SCN9A protein (p.Arg896Gln). The arginine residue is highly conserved and there is a … (more)
Pathogenic
(-)
no assertion criteria provided
Method: research
Indifference to pain, congenital, autosomal recessive
(Autosomal recessive inheritance)
Allele origin: maternal, unknown
Neuroalgology unit, Genetics of Neuropathic Pain Laboratory,Fondazione IRCCS Istituto Neurologico Carlo Besta
Accession: SCV001739272.1
Submitted: (Jun 30, 2021)
Evidence details
Publications
PubMed (2)

Functional evidence

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Functional consequence Method Result Submitter Supporting information
loss_of_function_variant
  1. molecular inversion probe-NGS
  2. Method not provided
  1. Result not provided
  2. Result not provided
Neuroalgology unit, Genetics of Neuropathic Pain Laboratory,Fondazione IRCCS Istituto Neurologico Carlo Besta
Accession: SCV001739272.1
Submitted: (Jun 30, 2021)
Evidence details
Publications
PubMed (2)

Citations for this variant

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Title Author Journal Year Link
A novel SCN9A splicing mutation in a compound heterozygous girl with congenital insensitivity to pain, hyposmia and hypogeusia. Marchi M Journal of the peripheral nervous system : JPNS 2018 PMID: 29978519
Congenital insensitivity to pain: novel SCN9A missense and in-frame deletion mutations. Cox JJ Human mutation 2010 PMID: 20635406

Text-mined citations for rs1024152367...

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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 Jul 07, 2021