NM_001379110.1(SLC9A6):c.67C>G (p.Leu23Val) AND Christianson syndrome

Germline classification:: Uncertain significance (1 submission)
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:: RCV002510626.2

Allele description [Variation Report for NM_001379110.1(SLC9A6):c.67C>G (p.Leu23Val)]

NM_001379110.1(SLC9A6):c.67C>G (p.Leu23Val)

Genes:

LOC130068747:ATAC-STARR-seq lymphoblastoid active region 29988 [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.67C>G (p.Leu23Val)

HGVS:

NC_000023.11:g.135985725C>G
NG_017160.2:g.16890C>G
NM_001042537.2:c.223C>G
NM_001177651.2:c.67C>G
NM_001330652.2:c.67C>G
NM_001379110.1:c.67C>GMANE SELECT
NM_001400909.1:c.67C>G
NM_001400910.1:c.67C>G
NM_001400911.1:c.67C>G
NM_001400912.1:c.67C>G
NM_001400913.1:c.67C>G
NM_006359.3:c.223C>G
NP_001036002.1:p.Leu75Val
NP_001171122.1:p.Leu23Val
NP_001317581.1:p.Leu23Val
NP_001366039.1:p.Leu23Val
NP_001387838.1:p.Leu23Val
NP_001387839.1:p.Leu23Val
NP_001387840.1:p.Leu23Val
NP_001387841.1:p.Leu23Val
NP_001387842.1:p.Leu23Val
NP_006350.1:p.Leu75Val
NC_000023.10:g.135067884C>G
NG_017160.1:g.5299C>G
NM_006359.2:c.223C>G

Protein change:

L23V

Molecular consequence:

NM_001042537.2:c.223C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001177651.2:c.67C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001330652.2:c.67C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001379110.1:c.67C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001400909.1:c.67C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001400910.1:c.67C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001400911.1:c.67C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001400912.1:c.67C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001400913.1:c.67C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_006359.3:c.223C>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Christianson syndrome (MRXSCH)
Synonyms:: MRXS Christianson; Angelman-like syndrome X-linked; Mental retardation microcephaly epilepsy and ataxia syndrome; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0010278; MedGen: C2678194; Orphanet: 85278; OMIM: 300243

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002820116	Neuberg Centre For Genomic Medicine, NCGM	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance	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

SCV002820116

Neuberg Centre For Genomic Medicine, NCGM

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance

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

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From Neuberg Centre For Genomic Medicine, NCGM, SCV002820116.1

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

Description

The missense variant p.L75V in SLC9A6 (NM_006359.3) has not been reported previously as a pathogenic variant nor as a benign variant, to our knowledge. The p.L75V variant is novel (not in any individuals) in gnomAD Exomes and is novel (not in any individuals) in 1000 Genomes. In silico predictions predict the variant to be damaging and the residue is conserved across species. For these reasons, this variant has been classified as Uncertain Significance.

#	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: Apr 6, 2024

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