NM_001379110.1(SLC9A6):c.-57+50G>T AND Christianson syndrome

Germline classification:: Benign (2 submissions)
Last evaluated:: Mar 26, 2021
Review status:: 3 stars out of maximum of 4 stars
reviewed by expert panel

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:: RCV000462225.26

Allele description [Variation Report for NM_001379110.1(SLC9A6):c.-57+50G>T]

NM_001379110.1(SLC9A6):c.-57+50G>T

Genes:

LOC130068746:ATAC-STARR-seq lymphoblastoid silent region 21025 [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.-57+50G>T

Other names:

p.A9S:GCA>TCA

HGVS:

NC_000023.11:g.135985527G>T
NG_017160.1:g.5101G>T
NM_001042537.2:c.25G>T
NM_001177651.2:c.-57+50G>T
NM_001330652.2:c.-57+55G>T
NM_001379110.1:c.-57+50G>TMANE SELECT
NM_006359.3:c.25G>T
NP_001036002.1:p.Ala9Ser
NP_001036002.1:p.Ala9Ser
NP_006350.1:p.Ala9Ser
NC_000023.10:g.135067686G>T
NM_001042537.1(SLC9A6):c.25G>T
NM_001042537.1:c.25G>T
NM_006359.2:c.25G>T

Protein change:

A9S

Links:

dbSNP: rs201523857

NCBI 1000 Genomes Browser:

rs201523857

Molecular consequence:

NM_001177651.2:c.-57+50G>T - intron variant - [Sequence Ontology: SO:0001627]
NM_001330652.2:c.-57+55G>T - intron variant - [Sequence Ontology: SO:0001627]
NM_001379110.1:c.-57+50G>T - intron variant - [Sequence Ontology: SO:0001627]
NM_001042537.2:c.25G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_006359.3:c.25G>T - 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
SCV000560949	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Benign (Feb 1, 2024)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV001711970	ClinGen Rett and Angelman-like Disorders Variant Curation Expert Panel	reviewed by expert panel (ClinGen RettAS ACMG Specifications V1)	Benign (Mar 26, 2021)	germline	curation	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000560949

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Benign
(Feb 1, 2024)

germline

clinical testing

PubMed (1)
[See all records that cite this PMID]

SCV001711970

ClinGen Rett and Angelman-like Disorders Variant Curation Expert Panel

reviewed by expert panel

(ClinGen RettAS ACMG Specifications V1)

Benign
(Mar 26, 2021)

germline

curation

Citation Link

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, curation

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 Labcorp Genetics (formerly Invitae), Labcorp, SCV000560949.9

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

#	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

From ClinGen Rett and Angelman-like Disorders Variant Curation Expert Panel, SCV001711970.1

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

Description

The allele frequency of the p.Ala9Ser variant in SLC9A6 is 0.307% in gnomAD, which is high enough to be classified as benign based on thresholds defined by the ClinGen Rett/Angelman-like Expert Panel for Rett/AS-like conditions (BA1). Computational analysis prediction tools suggest that the p.Ala9Ser variant does not have a deleterious impact; however this information does not predict clinical significance on its own (BP4). In summary, the p.Ala9Ser variant in SLC9A6 is classified as benign based on the ACMG/AMP criteria (BA1, BP4).

#	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: Oct 26, 2024

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