NM_003098.3(SNTA1):c.1388T>G (p.Leu463Arg) AND not provided

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jul 5, 2017
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:: RCV000520393.1

Allele description [Variation Report for NM_003098.3(SNTA1):c.1388T>G (p.Leu463Arg)]

NM_003098.3(SNTA1):c.1388T>G (p.Leu463Arg)

Gene:

SNTA1:syntrophin alpha 1 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

20q11.21

Genomic location:

Preferred name:

NM_003098.3(SNTA1):c.1388T>G (p.Leu463Arg)

HGVS:

NC_000020.11:g.33408738A>C
NG_011622.1:g.40155T>G
NM_003098.3:c.1388T>GMANE SELECT
NP_003089.1:p.Leu463Arg
NP_003089.1:p.Leu463Arg
LRG_332t1:c.1388T>G
LRG_332:g.40155T>G
LRG_332p1:p.Leu463Arg
NC_000020.10:g.31996544A>C
NM_003098.2:c.1388T>G

Protein change:

L463R

Links:

dbSNP: rs188835994

NCBI 1000 Genomes Browser:

rs188835994

Molecular consequence:

NM_003098.3:c.1388T>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000618086	GeneDx	criteria provided, single submitter (GeneDx Variant Classification (06012015))	Uncertain significance (Jul 5, 2017)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000618086

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification (06012015))

Uncertain significance
(Jul 5, 2017)

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	yes	not provided	not provided	not provided	not provided	not provided	clinical testing

Details of each submission

From GeneDx, SCV000618086.2

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

Description

The L463R variant of uncertain significance in the SNTA1 gene has not been published as pathogenic or been reported as benign to our knowledge. This variant has been identified in conjunction with a KCNH2 pathogenic variant in one other proband referred for LQTS testing at GeneDx. L463R has been observed in 5/11,572 (0.04%) alleles from individuals of Latino ancestry in the Exome Aggregation Consortium (Lek et al., 2016). The L463R variant is a non-conservative amino acid substitution, which is likely to impact secondary protein structure as these residues differ in polarity, charge, size and/or other properties. Moreover, this substitution occurs at a position that is conserved in mammals. However, in silico analysis is inconsistent in its predictions as to whether or not the variant is damaging to the protein structure/function.

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

Last Updated: May 1, 2024

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