NM_001379110.1(SLC9A6):c.-57+26A>G AND Christianson syndrome

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Mar 2, 2020
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:: RCV001058825.8

Allele description [Variation Report for NM_001379110.1(SLC9A6):c.-57+26A>G]

NM_001379110.1(SLC9A6):c.-57+26A>G

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+26A>G

HGVS:

NC_000023.11:g.135985503A>G
NG_017160.1:g.5077A>G
NM_001042537.2:c.1A>G
NM_001177651.2:c.-57+26A>G
NM_001330652.2:c.-57+31A>G
NM_001379110.1:c.-57+26A>GMANE SELECT
NM_006359.3:c.1A>G
NP_001036002.1:p.Met1Val
NP_001036002.1:p.Met1Val
NP_006350.1:p.Met1Val
NC_000023.10:g.135067662A>G
NM_001042537.1:c.1A>G
NM_006359.2:c.1A>G

Protein change:

M1V

Links:

dbSNP: rs782640388

NCBI 1000 Genomes Browser:

rs782640388

Molecular consequence:

NM_001042537.2:c.1A>G - initiator_codon_variant - [Sequence Ontology: SO:0001582]
NM_006359.3:c.1A>G - initiator_codon_variant - [Sequence Ontology: SO:0001582]
NM_001177651.2:c.-57+26A>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001330652.2:c.-57+31A>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001379110.1:c.-57+26A>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001042537.2:c.1A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_006359.3:c.1A>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

Recent activity

Clear Turn Off Turn On

cytochrome b, partial (mitochondrion) [Euoplos mcmillani]
cytochrome b, partial (mitochondrion) [Euoplos mcmillani]
gi|1142967982|gb|AQM32065.1|

Protein

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
SCV001223421	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Mar 2, 2020)	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

SCV001223421

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Mar 2, 2020)

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 Labcorp Genetics (formerly Invitae), Labcorp, SCV001223421.6

#	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. This variant has not been reported in the literature in individuals with SLC9A6-related conditions. The frequency data for this variant in the population databases is considered unreliable, as metrics indicate insufficient coverage at this position in the ExAC database. This sequence change affects the initiator methionine of the SLC9A6 mRNA. The next in-frame methionine is located at codon 25.

#	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 29, 2024

ClinVar

Relating variation to medicine