NM_001165963.4(SCN1A):c.5912A>G (p.Glu1971Gly) AND Inborn genetic diseases

Germline classification:: Likely benign (1 submission)
Last evaluated:: Mar 17, 2021
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:: RCV002514051.2

Allele description [Variation Report for NM_001165963.4(SCN1A):c.5912A>G (p.Glu1971Gly)]

NM_001165963.4(SCN1A):c.5912A>G (p.Glu1971Gly)

Genes:

SCN1A:sodium voltage-gated channel alpha subunit 1 [Gene - OMIM - HGNC]
LOC102724058:uncharacterized LOC102724058 [Gene]

Variant type:

single nucleotide variant

Cytogenetic location:

2q24.3

Genomic location:

Preferred name:

NM_001165963.4(SCN1A):c.5912A>G (p.Glu1971Gly)

Other names:

p.E1971G:GAA>GGA

HGVS:

NC_000002.12:g.165991363T>C
NG_011906.1:g.87277A>G
NM_001165963.4:c.5912A>GMANE SELECT
NM_001165964.3:c.5828A>G
NM_001202435.3:c.5912A>G
NM_001353948.2:c.5912A>G
NM_001353949.2:c.5879A>G
NM_001353950.2:c.5879A>G
NM_001353951.2:c.5879A>G
NM_001353952.2:c.5879A>G
NM_001353954.2:c.5876A>G
NM_001353955.2:c.5876A>G
NM_001353957.2:c.5828A>G
NM_001353958.2:c.5828A>G
NM_001353960.2:c.5825A>G
NM_001353961.2:c.3470A>G
NM_006920.6:c.5879A>G
NP_001159435.1:p.Glu1971Gly
NP_001159436.1:p.Glu1943Gly
NP_001189364.1:p.Glu1971Gly
NP_001340877.1:p.Glu1971Gly
NP_001340878.1:p.Glu1960Gly
NP_001340879.1:p.Glu1960Gly
NP_001340880.1:p.Glu1960Gly
NP_001340881.1:p.Glu1960Gly
NP_001340883.1:p.Glu1959Gly
NP_001340884.1:p.Glu1959Gly
NP_001340886.1:p.Glu1943Gly
NP_001340887.1:p.Glu1943Gly
NP_001340889.1:p.Glu1942Gly
NP_001340890.1:p.Glu1157Gly
NP_008851.3:p.Glu1960Gly
LRG_8:g.87277A>G
NC_000002.11:g.166847873T>C
NM_001165963.1:c.5912A>G
NR_148667.2:n.6329A>G

Protein change:

E1157G

Links:

dbSNP: rs771936735

NCBI 1000 Genomes Browser:

rs771936735

Molecular consequence:

NM_001165963.4:c.5912A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001165964.3:c.5828A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001202435.3:c.5912A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001353948.2:c.5912A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001353949.2:c.5879A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001353950.2:c.5879A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001353951.2:c.5879A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001353952.2:c.5879A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001353954.2:c.5876A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001353955.2:c.5876A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001353957.2:c.5828A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001353958.2:c.5828A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001353960.2:c.5825A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001353961.2:c.3470A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_006920.6:c.5879A>G - missense variant - [Sequence Ontology: SO:0001583]
NR_148667.2:n.6329A>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:: Inborn genetic diseases
Identifiers:: MeSH: D030342; MedGen: C0950123

Recent activity

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DA331023 BRHIP3 Homo sapiens cDNA clone BRHIP3028604 5', mRNA sequence
DA331023 BRHIP3 Homo sapiens cDNA clone BRHIP3028604 5', mRNA sequence
gi|78675967|gnl|dbEST|32956253|dbj| 023.1|

Nucleotide
Chain O, Non-complementary R-loop DNA strand
Chain O, Non-complementary R-loop DNA strand
gi|1545826453|pdb|6NE0|O

Nucleotide
Escherichia coli strain 729_180914_36s NODE_17_length_85173_cov_17.450180, whole...
Escherichia coli strain 729_180914_36s NODE_17_length_85173_cov_17.450180, whole genome shotgun sequence
gi|2783333194|ref|NZ_JBELNP01000001 gnl|WGS:NZ_JBELNP01|NODE_17_length_85173_cov_17.450180

Nucleotide
Homo sapiens transmembrane protein 211, mRNA (cDNA clone MGC:163521 IMAGE:401466...
Homo sapiens transmembrane protein 211, mRNA (cDNA clone MGC:163521 IMAGE:40146680), complete cds
gi|120659977|gb|BC130649.1|

Nucleotide
PREDICTED: Neomonachus schauinslandi glutathione S-transferase theta-3-like (LOC...
PREDICTED: Neomonachus schauinslandi glutathione S-transferase theta-3-like (LOC110578389), transcript variant X2, mRNA
gi|2128074476|ref|XM_044921120.1|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003754720	Ambry Genetics	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Likely benign (Mar 17, 2021)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 28518168, 32461654 Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003754720

Ambry Genetics

criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)

Likely benign
(Mar 17, 2021)

germline

clinical testing

PubMed (2)
[See all records that cite these PMIDs]

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

Citations

PubMed

Using high-resolution variant frequencies to empower clinical genome interpretation.

Whiffin N, Minikel E, Walsh R, O'Donnell-Luria AH, Karczewski K, Ing AY, Barton PJR, Funke B, Cook SA, MacArthur D, Ware JS.

Genet Med. 2017 Oct;19(10):1151-1158. doi: 10.1038/gim.2017.26. Epub 2017 May 18.

PubMed [citation]

PMID:: 28518168
PMCID:: PMC5563454

The mutational constraint spectrum quantified from variation in 141,456 humans.

Karczewski KJ, Francioli LC, Tiao G, Cummings BB, Alföldi J, Wang Q, Collins RL, Laricchia KM, Ganna A, Birnbaum DP, Gauthier LD, Brand H, Solomonson M, Watts NA, Rhodes D, Singer-Berk M, England EM, Seaby EG, Kosmicki JA, Walters RK, Tashman K, Farjoun Y, et al.

Nature. 2020 May;581(7809):434-443. doi: 10.1038/s41586-020-2308-7. Epub 2020 May 27. Erratum in: Nature. 2021 Feb;590(7846):E53. doi: 10.1038/s41586-020-03174-8. Nature. 2021 Sep;597(7874):E3-E4. doi: 10.1038/s41586-021-03758-y.

PubMed [citation]

PMID:: 32461654
PMCID:: PMC7334197

Details of each submission

From Ambry Genetics, SCV003754720.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (2)

Description

This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.

#	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: Sep 29, 2024

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