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_006922.4(SCN3A):c.2624T>C (p.Ile875Thr)

CA16043377

373960 (ClinVar)

Gene: SCN3A
Condition: developmental and epileptic encephalopathy
Inheritance Mode: Autosomal dominant inheritance
UUID: 2ec0b468-966c-4f4a-8b2b-75d4a680b3f1
Approved on: 2024-05-09
Published on: 2024-05-09

HGVS expressions

NM_006922.4:c.2624T>C
NM_006922.4(SCN3A):c.2624T>C (p.Ile875Thr)
NC_000002.12:g.165130238A>G
CM000664.2:g.165130238A>G
NC_000002.11:g.165986748A>G
CM000664.1:g.165986748A>G
NC_000002.10:g.165694994A>G
NG_042289.1:g.78851T>C
ENST00000706067.1:c.2573T>C
ENST00000283254.12:c.2624T>C
ENST00000638473.1:c.*465T>C
ENST00000639244.1:c.2573T>C
ENST00000640652.1:c.2573T>C
ENST00000658209.1:c.722T>C
ENST00000668657.1:c.2486T>C
ENST00000283254.11:c.2624T>C
ENST00000360093.7:c.2624T>C
ENST00000409101.7:c.2477T>C
ENST00000440431.6:c.2477T>C
NM_001081676.1:c.2477T>C
NM_001081677.1:c.2477T>C
NM_006922.3:c.2624T>C
NM_001081676.2:c.2477T>C
NM_001081677.2:c.2477T>C
More

Pathogenic

Met criteria codes 5
PM2_Supporting PS3 PS2_Very Strong PM6 PM1
Not Met criteria codes 4
BS1 BP4 BA1 PP3

Evidence Links 1

Expert Panel

Criteria Specification Information

Criteria Specification: ClinGen Epilepsy Sodium Channel Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for SCN3A Version 1.0.0

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Epilepsy Sodium Channel VCEP
The c.2624T>C variant in SCN3A is a missense variant predicted to cause substitution of isoleucine by threonine at amino acid 875 (p.Ile875Thr). The variant has been identified as a de novo occurrence with confirmed parental relationships in at least 4 individual(s) with DEE (PMIDs: 29740860, 29466837) (PS2_Very Strong) and as a de novo occurrance with unconfirmed parental relationship in a least 2 individuals with DEE (PMIDs: 29286531, 28191890) (PM6_Moderate), with additional case evidence available in the literature. The variant is absent from gnomAD v2.1.1 (PM2_Supporting). Studies have observed that when expressed in mammalian cells in culture, this variant causes a gain-of-function effect on the mutant channels as evidenced by a significant leftward/hyperpolarized shift in the voltage dependence of activation, an increase in the persistent/inactivating current, and a rightward/depolarizing shift in the voltage of inactivation (PS3; PMID: 29466837). In summary, this variant meets the criteria to be classified as pathogenic for autosomal dominant developmental and epilepstic encephalopathy based on the ACMG/AMP criteria applied, as specified by the ClinGen Epilepsy Sodium Channel VCEP: PS2_VS, PM6_Moderate, PM2_Supporting, PS3. (Version 1; July 7, 2023).
Met criteria codes
PM2_Supporting
This variant is absent from gnomAD v2.1.1.
PS3
Heterologous expression with voltage clamping showed a difference that exceeded the threshold for Strong in multiple biophysical parameters: Voltage dependence of activation shifted 10.9mV (WT -26.2; mutant -37.1), threshold 2.2mV. Voltage dependence of inactivation shifted 9.7mV (WT 10.2, mutant 19.9), threshold 4.1mV. Persistant current (WT 2.6, mutant 18.0) >135% of WT.

PS2_Very Strong
This variant has been identified as de novo via trio exome sequencing in at least 4 patients with consistent phenotypes.
PM6
This variant has been identified as de novo with confirmed parental relationships in at least 2 patients with consistent phenotypes.
PM1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
Not Met criteria codes
BS1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BA1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PP3
The in-silico REVEL score for this variant is 0.976 which meets the criteria for PP3_Moderate but was not applied as PM1_Strong was already reached.
Curation History
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