NM_001165963.4(SCN1A):c.1969_1975del (p.Pro657fs) AND Generalized epilepsy with febrile seizures plus, type 2

Germline classification:: Pathogenic (1 submission)
Last evaluated:: May 4, 2022
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

Somatic classification of clinical impact:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of oncogenicity:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Record status:: current
Accession:: RCV002250320.1

Allele description [Variation Report for NM_001165963.4(SCN1A):c.1969_1975del (p.Pro657fs)]

NM_001165963.4(SCN1A):c.1969_1975del (p.Pro657fs)

Gene:

SCN1A:sodium voltage-gated channel alpha subunit 1 [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

2q24.3

Genomic location:

Preferred name:

NM_001165963.4(SCN1A):c.1969_1975del (p.Pro657fs)

HGVS:

NC_000002.12:g.166043737_166043743del
NG_011906.1:g.34897_34903del
NM_001165963.4:c.1969_1975delMANE SELECT
NM_001165964.3:c.1959+10_1959+16del
NM_001202435.3:c.1969_1975del
NM_001353948.2:c.1969_1975del
NM_001353949.2:c.1969_1975del
NM_001353950.2:c.1969_1975del
NM_001353951.2:c.1969_1975del
NM_001353952.2:c.1969_1975del
NM_001353954.2:c.1966_1972del
NM_001353955.2:c.1966_1972del
NM_001353957.2:c.1959+10_1959+16del
NM_001353958.2:c.1959+10_1959+16del
NM_001353960.2:c.1956+10_1956+16del
NM_001353961.2:c.-457_-451del
NM_006920.6:c.1969_1975del
NP_001159435.1:p.Pro657fs
NP_001189364.1:p.Pro657fs
NP_001340877.1:p.Pro657fs
NP_001340878.1:p.Pro657fs
NP_001340879.1:p.Pro657fs
NP_001340880.1:p.Pro657fs
NP_001340881.1:p.Pro657fs
NP_001340883.1:p.Pro656fs
NP_001340884.1:p.Pro656fs
NP_008851.3:p.Pro657fs
LRG_8:g.34897_34903del
NC_000002.11:g.166900247_166900253del
NC_000002.12:g.166043737_166043743delCTGAAGG
NR_148667.2:n.2355_2361del

Protein change:

P656fs

Links:

dbSNP: rs2105841790

NCBI 1000 Genomes Browser:

rs2105841790

Molecular consequence:

NM_001353961.2:c.-457_-451del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001165963.4:c.1969_1975del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001202435.3:c.1969_1975del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001353948.2:c.1969_1975del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001353949.2:c.1969_1975del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001353950.2:c.1969_1975del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001353951.2:c.1969_1975del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001353952.2:c.1969_1975del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001353954.2:c.1966_1972del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001353955.2:c.1966_1972del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_006920.6:c.1969_1975del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001165964.3:c.1959+10_1959+16del - intron variant - [Sequence Ontology: SO:0001627]
NM_001353957.2:c.1959+10_1959+16del - intron variant - [Sequence Ontology: SO:0001627]
NM_001353958.2:c.1959+10_1959+16del - intron variant - [Sequence Ontology: SO:0001627]
NM_001353960.2:c.1956+10_1956+16del - intron variant - [Sequence Ontology: SO:0001627]
NR_148667.2:n.2355_2361del - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:: Generalized epilepsy with febrile seizures plus, type 2 (GEFSP2)
Synonyms:: GEFS+, TYPE 2
Identifiers:: MONDO: MONDO:0011461; MedGen: C1858673; Orphanet: 36387; OMIM: 604403

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002519035	Mendelics	criteria provided, single submitter (Mendelics Assertion Criteria 2019)	Pathogenic (May 4, 2022)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002519035

Mendelics

criteria provided, single submitter

(Mendelics Assertion Criteria 2019)

Pathogenic
(May 4, 2022)

germline

clinical testing

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Details of each submission

From Mendelics, SCV002519035.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Dec 24, 2023

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