The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]
  • Gene obtained from curated document aligns with the Allele Registry but not with ClinVar data
  • No CSPEC computed assertion could be determined for this classification!


Variant: NM_001165963.4(SCN1A):c.5797del (p.Arg1933fs)

CA269784

130208 (ClinVar)

Gene: SCN1A
Condition: generalized epilepsy with febrile seizures plus
Inheritance Mode: Autosomal dominant inheritance
UUID: 72aff15b-5ff5-4399-9e6f-458b3bf66854
Approved on: 2024-10-01
Published on: 2024-11-05

HGVS expressions

NM_001165963.4:c.5797del
NM_001165963.4(SCN1A):c.5797del (p.Arg1933fs)
NC_000002.12:g.165991478del
CM000664.2:g.165991478del
NC_000002.11:g.166847988del
CM000664.1:g.166847988del
NC_000002.10:g.166556234del
NG_011906.1:g.87162del
ENST00000689288.1:c.*3833del
ENST00000303395.9:c.5797del
ENST00000635750.1:c.5764del
ENST00000635776.1:c.*2630del
ENST00000636194.1:c.*3290del
ENST00000637038.1:c.2659del
ENST00000637988.1:c.5764del
ENST00000640036.1:c.5764del
ENST00000641575.1:c.5761del
ENST00000641603.1:c.5515del
ENST00000641996.1:c.*5351del
ENST00000671940.1:c.*3740del
ENST00000673490.1:n.8270del
ENST00000674923.1:c.5797del
ENST00000303395.8:c.5797del
ENST00000375405.7:c.5764del
ENST00000409050.1:c.5713del
ENST00000423058.6:c.5797del
NM_001165963.1:c.5797del
NM_001165964.1:c.5713del
NM_001202435.1:c.5797del
NM_006920.4:c.5764del
NR_110598.1:n.176-24135del
NM_001165963.2:c.5797del
NM_001165964.2:c.5713del
NM_001202435.2:c.5797del
NM_001353948.1:c.5797del
NM_001353949.1:c.5764del
NM_001353950.1:c.5764del
NM_001353951.1:c.5764del
NM_001353952.1:c.5764del
NM_001353954.1:c.5761del
NM_001353955.1:c.5761del
NM_001353957.1:c.5713del
NM_001353958.1:c.5713del
NM_001353960.1:c.5710del
NM_001353961.1:c.3355del
NM_006920.5:c.5764del
NR_148667.1:n.6233del
NM_001165963.3:c.5797del
NM_001165964.3:c.5713del
NM_001202435.3:c.5797del
NM_001353948.2:c.5797del
NM_001353949.2:c.5764del
NM_001353950.2:c.5764del
NM_001353951.2:c.5764del
NM_001353952.2:c.5764del
NM_001353954.2:c.5761del
NM_001353955.2:c.5761del
NM_001353957.2:c.5713del
NM_001353958.2:c.5713del
NM_001353960.2:c.5710del
NM_001353961.2:c.3355del
NM_006920.6:c.5764del
NR_148667.2:n.6214del
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Uncertain Significance

Met criteria codes 1
PM2
Not Met criteria codes 2
PVS1 PS4

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specification: ClinGen Epilepsy Sodium Channel Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for SCN1A Version 1.0.0

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Epilepsy Sodium Channel VCEP
The c.5797del variant in SCN1A is a single nucleotide deletion predicted to cause a frameshift at amino acid position 1933 leading to a premature stop codon (p.Arg1933Glufs*3). The variant is located within the last exon and thus predicted to escape nonsense mediated decay. The truncated region is not known to be important for protein function, as missense variants reported in the region do not meet PLP per these criteria. Furthermore, LOF variants within this exon are relatively common in gnomAD v4.1. As such, this variant does not meet criteria to apply PVS1. This variant has been identified in a family in which 2 affected siblings with developmental and epileptic encephalopathy (DEE) harbored the variant, in addition to an unaffected parent and 2 unaffected siblings (LabCorp Genetics, Inc. internal data). Given the severity of the phenotype and presence in multiple unaffected family members, this case was not included as evidence for PS4. The variant is absent from the population database, gnomAD v4.1 (PM2_Supporting). In summary, this variant meets the criteria to be classified as Variant of Uncertain Significance for autosomal dominant SCN1A-related disorder, based on the ACMG/AMP criteria applied, as specified by the ClinGen Epilepsy Sodium Channel VCEP: PM2_Supporting. (version 1.0, approved September 24, 2024).
Met criteria codes
PM2
This variant is absent from gnomAD v4.1. However, we note that c.5797C>T (p.Arg1933Ter) variant is present in 4 individuals 0.0002%
Not Met criteria codes
PVS1
frameshift variant, not predicted to undergo NMD. Truncated/latered region is not critical to protein function (while other missense variants downstream have been reported, none meet PLP per our criteria). LOF variants are relatively frequenct in gnomAD, most cluster in last exon.
PS4
Lapcorp Geneitcs, Inc.: identified in 1 internal family with 2 siblings who both have a DEE phenotype. It has also been observed in an unaffected parent and 2 unaffected siblings. Given the severity of the phenotype in the affected individuals and presence in unaffected family members, this case was not included as evidence.
Curation History
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