rs1060502049
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Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PVS1_ModeratePM2
The NM_001365536.1(SCN9A):c.5897_5900dupAAGA(p.Lys1968fs) variant causes a frameshift change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000132 in 152,038 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.000013 ( 0 hom., cov: 32)
Consequence
SCN9A
NM_001365536.1 frameshift
NM_001365536.1 frameshift
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 8.01
Genes affected
SCN9A (HGNC:10597): (sodium voltage-gated channel alpha subunit 9) This gene encodes a voltage-gated sodium channel which plays a significant role in nociception signaling. Mutations in this gene have been associated with primary erythermalgia, channelopathy-associated insensitivity to pain, and paroxysmal extreme pain disorder. [provided by RefSeq, Aug 2009]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 4 ACMG points.
PVS1
Loss of function variant, product does not undergo nonsense mediated mRNA decay. Variant is located in the 3'-most exon, not predicted to undergo nonsense mediated mRNA decay. Fraction of 0.0112 CDS is truncated, and there are 0 pathogenic variants in the truncated region.
PM2
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SCN9A | NM_001365536.1 | c.5897_5900dupAAGA | p.Lys1968fs | frameshift_variant | 27/27 | ENST00000642356.2 | NP_001352465.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SCN9A | ENST00000642356.2 | c.5897_5900dupAAGA | p.Lys1968fs | frameshift_variant | 27/27 | NM_001365536.1 | ENSP00000495601.1 | |||
SCN9A | ENST00000303354.11 | c.5897_5900dupAAGA | p.Lys1968fs | frameshift_variant | 27/27 | 5 | ENSP00000304748.7 | |||
SCN9A | ENST00000409672.5 | c.5864_5867dupAAGA | p.Lys1957fs | frameshift_variant | 27/27 | 5 | ENSP00000386306.1 | |||
SCN9A | ENST00000645907.1 | c.5864_5867dupAAGA | p.Lys1957fs | frameshift_variant | 27/27 | ENSP00000495983.1 |
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 152038Hom.: 0 Cov.: 32
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GnomAD4 exome Cov.: 32
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GnomAD4 genome AF: 0.0000132 AC: 2AN: 152038Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74260
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Generalized epilepsy with febrile seizures plus, type 7;C2752089:Neuropathy, hereditary sensory and autonomic, type 2A Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Mar 14, 2017 | This sequence change inserts 4 nucleotide in exon 27 of the SCN9A mRNA (c.5864_5867dupAAGA), causing a frameshift at codon 1957. This creates a premature translational stop signal in the last exon of the SCN9A mRNA (p.Lys1957Argfs*4). While this is not anticipated to result in nonsense mediated decay, it is expected to disrupt the last 21 amino acids of the SCN9A protein. In summary, this variant is a novel truncation with uncertain impact on protein function. It has been classified as a Variant of Uncertain Significance. Experimental studies have not been reported for this truncating variant and it is currently unknown if the last 21 amino acids of the SCN9A protein are critical for its function. This variant is not present in population databases (ExAC no frequency) and has not been reported in the literature in individuals with a SCN9A-related disease. - |
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Find out detailed SpliceAI scores and Pangolin per-transcript scores at