rs1553488759

Variant names:

• chr2-166280376-A-ACATTTTTGAATTCCTCAGT
• rs1553488759
• NM_001365536.1:c.2305_2323dupACTGAGGAATTCAAAAATG

Variant summary

Our verdict is Pathogenic. The variant received 10 ACMG points: 10P and 0B. PVS1 PP5_Moderate

The NM_001365536.1(SCN9A):​c.2305_2323dupACTGAGGAATTCAAAAATG​(p.Val775AspfsTer2) variant causes a frameshift, stop gained change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. It is difficult to determine the true allele frequency of this variant because it is of type INS_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. Variant has been reported in ClinVar as Pathogenic (★). Synonymous variant affecting the same amino acid position (i.e. V775V) has been classified as Likely benign. Variant results in nonsense mediated mRNA decay.

• Frequency: Genomes: not found (cov: 33)
• Consequence: SCN9A NM_001365536.1 frameshift, stop_gained
• Clinical Significance: Pathogenic criteria provided, single submitter P:1
• Conservation: PhyloP100: 1.47
• Publications: 0 publications found

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]

SCN1A-AS1 (HGNC:54069): (SCN1A and SCN9A antisense RNA 1)

ACMG classification

Our verdict: Pathogenic. The variant received 10 ACMG points.

• PVS1: Loss of function variant, product undergoes nonsense mediated mRNA decay. LoF is a known mechanism of disease.
• PP5: Variant 2-166280376-A-ACATTTTTGAATTCCTCAGT is Pathogenic according to our data. Variant chr2-166280376-A-ACATTTTTGAATTCCTCAGT is described in ClinVar as Pathogenic. ClinVar VariationId is 471095.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SCN9A	NM_001365536.1	c.2305_2323dupACTGAGGAATTCAAAAATG	p.Val775AspfsTer2	frameshift_variant, stop_gained	Exon 14 of 27	ENST00000642356.2	NP_001352465.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SCN9A	ENST00000642356.2	c.2305_2323dupACTGAGGAATTCAAAAATG	p.Val775AspfsTer2	frameshift_variant, stop_gained	Exon 14 of 27		NM_001365536.1	ENSP00000495601.1
SCN9A	ENST00000303354.11	c.2305_2323dupACTGAGGAATTCAAAAATG	p.Val775AspfsTer2	frameshift_variant, stop_gained	Exon 14 of 27	5		ENSP00000304748.7
SCN9A	ENST00000409672.5	c.2272_2290dupACTGAGGAATTCAAAAATG	p.Val764AspfsTer2	frameshift_variant, stop_gained	Exon 14 of 27	5		ENSP00000386306.1
SCN9A	ENST00000645907.1	c.2272_2290dupACTGAGGAATTCAAAAATG	p.Val764AspfsTer2	frameshift_variant, stop_gained	Exon 14 of 27			ENSP00000495983.1
SCN9A	ENST00000454569.6	c.2272_2290dupACTGAGGAATTCAAAAATG	p.Val764AspfsTer2	frameshift_variant, stop_gained	Exon 14 of 15	1		ENSP00000413212.2

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 30

GnomAD4 genome Cov.: 33

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:1

Revision: criteria provided, single submitter

Submissions by phenotype

Generalized epilepsy with febrile seizures plus, type 7;C2752089:Neuropathy, hereditary sensory and autonomic, type 2A Pathogenic:1

Jan 11, 2022

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This sequence change creates a premature translational stop signal (p.Val764Aspfs*2) in the SCN9A gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in SCN9A are known to be pathogenic (PMID: 17470132, 19304393). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with SCN9A-related conditions. ClinVar contains an entry for this variant (Variation ID: 471095). For these reasons, this variant has been classified as Pathogenic. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		1.5
Mutation Taster		=0/200	disease causing (ClinVar)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs1553488759; hg19: chr2-167136886;