NM_030962.4(SBF2):c.5375C>T (p.Ala1792Val) AND Charcot-Marie-Tooth disease type 4

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

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jul 31, 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:: RCV000555438.11

Allele description

NM_030962.4(SBF2):c.5375C>T (p.Ala1792Val)

Genes:

SBF2-AS1:SBF2 antisense RNA 1 [Gene - HGNC]
SBF2:SET binding factor 2 [Gene - OMIM - HGNC]
LOC105369149:uncharacterized LOC105369149 [Gene]

Variant type:

single nucleotide variant

Cytogenetic location:

11p15.4

Genomic location:

Preferred name:

NM_030962.4(SBF2):c.5375C>T (p.Ala1792Val)

HGVS:

NC_000011.10:g.9781583G>A
NG_008074.1:g.517625C>T
NM_001386339.1:c.5471C>T
NM_001386342.1:c.5246C>T
NM_030962.4:c.5375C>TMANE SELECT
NP_001373268.1:p.Ala1824Val
NP_001373271.1:p.Ala1749Val
NP_112224.1:p.Ala1792Val
NP_112224.1:p.Ala1792Val
LRG_267t1:c.5375C>T
LRG_267:g.517625C>T
LRG_267p1:p.Ala1792Val
NC_000011.9:g.9803130G>A
NM_030962.3:c.5375C>T

Protein change:

A1749V

Links:

dbSNP: rs1554897834

NCBI 1000 Genomes Browser:

rs1554897834

Molecular consequence:

NM_001386339.1:c.5471C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001386342.1:c.5246C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_030962.4:c.5375C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Charcot-Marie-Tooth disease type 4
Synonyms:: Charcot-Marie-Tooth, Type 4
Identifiers:: MONDO: MONDO:0018995; MedGen: C4082197

Recent activity

Clear Turn Off Turn On

SEMA7A [Otolemur garnettii]
SEMA7A [Otolemur garnettii]
Gene ID:100952899

Gene

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

Help

Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000657972	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Jul 31, 2021)	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

SCV000657972

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Jul 31, 2021)

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, SCV000657972.7

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

Description

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. Algorithms developed to predict the effect of missense changes on protein structure and function do not agree on the potential impact of this missense change (SIFT: "Tolerated"; PolyPhen-2: "Possibly Damaging"; Align-GVGD: "Class C0"). This variant has not been reported in the literature in individuals with SBF2-related disease. ClinVar contains an entry for this variant (Variation ID: 476937). This variant is not present in population databases (ExAC no frequency). This sequence change replaces alanine with valine at codon 1792 of the SBF2 protein (p.Ala1792Val). The alanine residue is highly conserved and there is a small physicochemical difference between alanine and valine.

#	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 1, 2024

ClinVar

Relating variation to medicine