NM_000335.5(SCN5A):c.3020C>T (p.Thr1007Ile) AND not provided

This record was updated by the submitter. Please see the current version.

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jan 25, 2024
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:: RCV003539362.2

Allele description

NM_000335.5(SCN5A):c.3020C>T (p.Thr1007Ile)

Genes:

LOC110121269:VISTA enhancer hs2177 [Gene]
SCN5A:sodium voltage-gated channel alpha subunit 5 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

3p22.2

Genomic location:

Preferred name:

NM_000335.5(SCN5A):c.3020C>T (p.Thr1007Ile)

HGVS:

NC_000003.12:g.38581139G>A
NG_008934.1:g.73534C>T
NG_053884.1:g.2878G>A
NM_000335.5:c.3020C>TMANE SELECT
NM_001099404.2:c.3020C>T
NM_001099405.2:c.3020C>T
NM_001160160.2:c.3020C>T
NM_001160161.2:c.3020C>T
NM_001354701.2:c.3020C>T
NM_198056.3:c.3020C>T
NP_000326.2:p.Thr1007Ile
NP_001092874.1:p.Thr1007Ile
NP_001092875.1:p.Thr1007Ile
NP_001153632.1:p.Thr1007Ile
NP_001153633.1:p.Thr1007Ile
NP_001341630.1:p.Thr1007Ile
NP_932173.1:p.Thr1007Ile
NP_932173.1:p.Thr1007Ile
LRG_289t1:c.3020C>T
LRG_289:g.73534C>T
LRG_289p1:p.Thr1007Ile
NC_000003.11:g.38622630G>A
NM_198056.2:c.3020C>T

Protein change:

T1007I

Links:

dbSNP: rs763935970

NCBI 1000 Genomes Browser:

rs763935970

Molecular consequence:

NM_000335.5:c.3020C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001099404.2:c.3020C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001099405.2:c.3020C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001160160.2:c.3020C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001160161.2:c.3020C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001354701.2:c.3020C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_198056.3:c.3020C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

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SRX22108360 (1)
SRA
SRX23842565 (1)
SRA
Mus musculus HNF1 homeobox B (Hnf1b), transcript variant 2, mRNA
Mus musculus HNF1 homeobox B (Hnf1b), transcript variant 2, mRNA
gi|602152748|ref|NM_001291268.1|

Nucleotide
AL655549 XGC-neurula Xenopus tropicalis cDNA clone TNeu030b08 5', mRNA sequence
AL655549 XGC-neurula Xenopus tropicalis cDNA clone TNeu030b08 5', mRNA sequence
gi|38223434|gnl|dbEST|20325973|emb| 549.2|

Nucleotide
LOC127893138 [Homo sapiens]
LOC127893138 [Homo sapiens]
Gene ID:127893138

Gene

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000964695	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Jan 25, 2024)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000964695

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Jan 25, 2024)

germline

clinical testing

PubMed (1)
[See all records that cite this PMID]

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

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Invitae, SCV000964695.3

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

Description

This sequence change replaces threonine, which is neutral and polar, with isoleucine, which is neutral and non-polar, at codon 1007 of the SCN5A protein (p.Thr1007Ile). This variant is present in population databases (rs763935970, gnomAD 0.0009%). This variant has not been reported in the literature in individuals affected with SCN5A-related conditions. ClinVar contains an entry for this variant (Variation ID: 665520). An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant¬†is likely to be tolerated. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.

#	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 16, 2024

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