NM_001365536.1(SCN9A):c.4629_4631delinsAGA (p.Met1543_Thr1544delinsIleAsp) AND multiple conditions

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Oct 5, 2023
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:: RCV001243232.2

Allele description [Variation Report for NM_001365536.1(SCN9A):c.4629_4631delinsAGA (p.Met1543_Thr1544delinsIleAsp)]

NM_001365536.1(SCN9A):c.4629_4631delinsAGA (p.Met1543_Thr1544delinsIleAsp)

Genes:

SCN1A-AS1:SCN1A and SCN9A antisense RNA 1 [Gene - HGNC]
SCN9A:sodium voltage-gated channel alpha subunit 9 [Gene - OMIM - HGNC]

Variant type:

Indel

Cytogenetic location:

2q24.3

Genomic location:

Preferred name:

NM_001365536.1(SCN9A):c.4629_4631delinsAGA (p.Met1543_Thr1544delinsIleAsp)

HGVS:

NC_000002.12:g.166204098_166204100delinsTCT
NG_012798.1:g.176888_176890delinsAGA
NM_001365536.1:c.4629_4631delinsAGAMANE SELECT
NM_002977.4:c.4596_4598delGACinsAGA
NP_001352465.1:p.Met1543_Thr1544delinsIleAsp
NP_002968.1:p.Met1532_Thr1533delinsIleAsp
NP_002968.1:p.Met1532_Thr1533delinsIleAsp
NP_002968.2:p.Met1532_Thr1533delinsIleAsp
LRG_369t1:c.4596_4598delinsAGA
LRG_369:g.176888_176890delinsAGA
LRG_369p1:p.Met1532_Thr1533delinsIleAsp
NC_000002.11:g.167060608_167060610delinsTCT
NC_000002.11:g.167060608_167060610delinsTCT
NM_002977.2:c.4596_4598delGACinsAGA
NM_002977.3:c.4596_4598delinsAGA

Links:

dbSNP: rs1693675341

NCBI 1000 Genomes Browser:

rs1693675341

Molecular consequence:

NM_001365536.1:c.4629_4631delinsAGA - missense variant - [Sequence Ontology: SO:0001583]
NM_002977.4:c.4596_4598delGACinsAGA - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Neuropathy, hereditary sensory and autonomic, type 2A (HSAN2A)
Synonyms:: ACROOSTEOLYSIS, GIACCAI TYPE; ACROOSTEOLYSIS, NEUROGENIC; HSAN IIA; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0024309; MedGen: C2752089; Orphanet: 970; OMIM: 201300

Name:: Generalized epilepsy with febrile seizures plus, type 7 (GEFSP7)
Synonyms:: GEFS+, TYPE 7
Identifiers:: MONDO: MONDO:0013470; MedGen: C2751778; Orphanet: 36387; OMIM: 613863

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001416375	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Oct 5, 2023)	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

SCV001416375

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Oct 5, 2023)

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):240-242.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Invitae, SCV001416375.2

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

Description

This variant, c.4596_4598delinsAGA, is a complex sequence change that results in the deletion of 2 and insertion of 2 amino acid(s) in the SCN9A protein (p.Met1532_Thr1533delinsIleAsp). Information on the frequency of this variant in the gnomAD database is not available, as this variant may be reported differently in the database. This variant has not been reported in the literature in individuals affected with SCN9A-related conditions. ClinVar contains an entry for this variant (Variation ID: 968165). Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. 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: Mar 5, 2024

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