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 computer assertion could be determined for this classification!


Variant: NM_001165963.4(SCN1A):c.4916G>C (p.Arg1639Pro)

CA317553

206852 (ClinVar)

Gene: SCN1A
Condition: Dravet syndrome
Inheritance Mode: Autosomal dominant inheritance
UUID: a5e68076-bd6c-486e-b7d7-2efd3af6caa5
Approved on: 2024-05-09
Published on: 2024-05-09

HGVS expressions

NM_001165963.4:c.4916G>C
NM_001165963.4(SCN1A):c.4916G>C (p.Arg1639Pro)
NC_000002.12:g.165992359C>G
CM000664.2:g.165992359C>G
NC_000002.11:g.166848869C>G
CM000664.1:g.166848869C>G
NC_000002.10:g.166557115C>G
NG_011906.1:g.86281G>C
ENST00000689288.1:c.*2952G>C
ENST00000303395.9:c.4916G>C
ENST00000635750.1:c.4883G>C
ENST00000635776.1:c.*1749G>C
ENST00000636194.1:c.*2409G>C
ENST00000637038.1:c.1778G>C
ENST00000637988.1:c.4883G>C
ENST00000640036.1:c.4883G>C
ENST00000641575.1:c.4880G>C
ENST00000641603.1:c.4634G>C
ENST00000641996.1:c.*4470G>C
ENST00000671940.1:c.*2859G>C
ENST00000673490.1:n.7389G>C
ENST00000674923.1:c.4916G>C
ENST00000303395.8:c.4916G>C
ENST00000375405.7:c.4883G>C
ENST00000409050.1:c.4832G>C
ENST00000423058.6:c.4916G>C
NM_001165963.1:c.4916G>C
NM_001165964.1:c.4832G>C
NM_001202435.1:c.4916G>C
NM_006920.4:c.4883G>C
NR_110598.1:n.176-23254C>G
NM_001165963.2:c.4916G>C
NM_001165964.2:c.4832G>C
NM_001202435.2:c.4916G>C
NM_001353948.1:c.4916G>C
NM_001353949.1:c.4883G>C
NM_001353950.1:c.4883G>C
NM_001353951.1:c.4883G>C
NM_001353952.1:c.4883G>C
NM_001353954.1:c.4880G>C
NM_001353955.1:c.4880G>C
NM_001353957.1:c.4832G>C
NM_001353958.1:c.4832G>C
NM_001353960.1:c.4829G>C
NM_001353961.1:c.2474G>C
NM_006920.5:c.4883G>C
NR_148667.1:n.5352G>C
NM_001165963.3:c.4916G>C
NM_001165964.3:c.4832G>C
NM_001202435.3:c.4916G>C
NM_001353948.2:c.4916G>C
NM_001353949.2:c.4883G>C
NM_001353950.2:c.4883G>C
NM_001353951.2:c.4883G>C
NM_001353952.2:c.4883G>C
NM_001353954.2:c.4880G>C
NM_001353955.2:c.4880G>C
NM_001353957.2:c.4832G>C
NM_001353958.2:c.4832G>C
NM_001353960.2:c.4829G>C
NM_001353961.2:c.2474G>C
NM_006920.6:c.4883G>C
NR_148667.2:n.5333G>C

Pathogenic

Met criteria codes 5
PM1 PS4_Moderate PP3_Moderate PM5_Strong PM2_Supporting
Not Met criteria codes 13
BP5 BP2 PM3 PS2 PS1 PS3 PM6 BA1 PP1 BS4 BS3 BS1 BS2

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.4916G>C variant in SCN1A is a missense variant predicted to cause substitution of arginine by proline at amino acid 1639 (p.Arg1639Pro). This variant has been reported in at least one individual with Dravet syndrome and another individual with epilepsy with no additional details (PMIDs:35087721, 29655203) (PS4_Moderate). Multiple missense variants in SCN1A and in paralogous genes have previously been reported and meet P/LP per these criteria, including SCN1A: p.R1639G (PMIDs:18930999), SCN2A: p.R1629L, p.R1629H and SCN8A: p.R1620L (PMIDs 28330790, 3061509). (PM5_Strong). An identical amino acid substitution at the corresponding position in the paralogous gene, SCN2A has been reported as de novo (p.R1629P), however this did not meet P/LP per these criteria so PS1 was not met. This variant is absent from the population database, gnomAD v2.1.1 (PM2_Supporting). It falls within a pathogenic enriched region that is defined as a mutational hotspot (PM1). The computational predictor REVEL gives a score of 0.98, which is above the threshold of 0.773, evidence that correlates with a maximum strength of PP3_Moderate. In summary, this variant meets the criteria to be classified as pathogenic for autosomal dominant Dravet syndrome based on the ACMG/AMP criteria applied, as specified by the ClinGen Epilepsy Sodium Channel VCEP: PS4_Moderate, PM5_Strong, PM1, PM2_Supporting, PP3_Moderate (version 1.0; 5/9/23).
Met criteria codes
PM1
Located in a pathogenic enriched region.
PS4_Moderate
Multiple unrelated probands with consistent phenotypes. Identified in 1 patient with Dravet syndrome (2 points) and 1 patient with epilepsy NOS (0.25 points).
PP3_Moderate
REVEL = 0.98
PM5_Strong
SCN1A:R1639G reported in PMID:18930999 . Can also utilize non-identical substitutions in paralogous NDD genes. SCN2A:R1629L,R1629H muliple reports each of DEE; SCN8A:R1620L de novo ASD PMID:28330790 w/functional characterization PMID:30615093
PM2_Supporting
Absent from population databases
Not Met criteria codes
BP5
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PS2
No de novo cases have been reported
PS1
Can also utilize identical aa substitutions in paralogous genes. Symonds- SCN2A:R1629P de novo West syndrome, although this would unlikely meet LP per these criteria so this was not applied.
PS3
Variant has not been functionally characterized.
PM6
No de novo cases have been reported
BA1
Absent from population databases
PP1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BS4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BS3
Not applicable, also variant has not been functionally characterized.
BS1
Absent from population databases
BS2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
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