NM_001379110.1(SLC9A6):c.1599A>C (p.Glu533Asp) AND not provided

Germline classification:: Uncertain significance (2 submissions)
Last evaluated:: Jul 3, 2014
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV000723930.5

Allele description [Variation Report for NM_001379110.1(SLC9A6):c.1599A>C (p.Glu533Asp)]

NM_001379110.1(SLC9A6):c.1599A>C (p.Glu533Asp)

Gene:

SLC9A6:solute carrier family 9 member A6 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

Xq26.3

Genomic location:

Preferred name:

NM_001379110.1(SLC9A6):c.1599A>C (p.Glu533Asp)

Other names:

p.E523D:GAA>GAC

HGVS:

NC_000023.11:g.136033431A>C
NG_017160.1:g.53005A>C
NM_001042537.2:c.1665A>C
NM_001177651.2:c.1509A>C
NM_001330652.2:c.1413A>C
NM_001379110.1:c.1599A>CMANE SELECT
NM_006359.3:c.1569A>C
NP_001036002.1:p.Glu555Asp
NP_001171122.1:p.Glu503Asp
NP_001317581.1:p.Glu471Asp
NP_001366039.1:p.Glu533Asp
NP_006350.1:p.Glu523Asp
NC_000023.10:g.135115590A>C
NM_006359.2:c.1569A>C

Protein change:

E471D

Links:

dbSNP: rs781949645

NCBI 1000 Genomes Browser:

rs781949645

Molecular consequence:

NM_001042537.2:c.1665A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001177651.2:c.1509A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001330652.2:c.1413A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001379110.1:c.1599A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_006359.3:c.1569A>C - missense variant - [Sequence Ontology: SO:0001583]

Observations:

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
SCV000226122	Eurofins Ntd Llc (ga)	criteria provided, single submitter (EGL Classification Definitions 2015)	Uncertain significance (Jul 3, 2014)	germline	clinical testing	Citation Link,
SCV000243052	GeneDx	criteria provided, single submitter (GeneDx Variant Classification (06012015))	Uncertain significance (Mar 6, 2014)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000226122

Eurofins Ntd Llc (ga)

criteria provided, single submitter

(EGL Classification Definitions 2015)

Uncertain significance
(Jul 3, 2014)

germline

clinical testing

Citation Link,

SCV000243052

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification (06012015))

Uncertain significance
(Mar 6, 2014)

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
not provided	germline	unknown	1	not provided	not provided	not provided	not provided	clinical testing

Details of each submission

From Eurofins Ntd Llc (ga), SCV000226122.5

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

#	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		1	not provided	not provided	not provided

From GeneDx, SCV000243052.10

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

Description

p.Glu523Asp (GAA>GAC): c.1569 A>C in exon 14 of the SLC9A6 gene (NM_006359.2) A variant of unknown significance has been identified in the SLC9A6 gene. The E523D variant has not been published as a mutation, nor has it been reported as a benign polymorphism to our knowledge. It was not observed in approximately 6,500 individuals of European and African American ancestry in the NHLBI Exome Sequencing Project, indicating it is not a common benign variant in these populations. The E523D variant is a conservative amino acid substitution, which is not likely to impact secondary protein structure as these residues share similar properties. In addition, other nearby missense mutations have not been reported in association with epilepsy. However, this substitution occurs at a position that is highly conserved across species. In silico analysis is inconsistent in its predictions as to whether or not the variant is damaging to the protein structure/function. Therefore, based on the currently available information, it is unclear whether this variant is a pathogenic mutation or a rare benign variant. The variant is found in CHILD-EPI panel(s).

#	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: Feb 28, 2024

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