NM_001379110.1(SLC9A6):c.-56-22C>T AND Christianson syndrome

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Dec 17, 2022
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:: RCV003625359.2

Allele description [Variation Report for NM_001379110.1(SLC9A6):c.-56-22C>T]

NM_001379110.1(SLC9A6):c.-56-22C>T

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.-56-22C>T

HGVS:

NC_000023.11:g.135985581C>T
NG_017160.1:g.5155C>T
NG_017160.2:g.16746C>T
NG_203160.1:g.356C>T
NM_001042537.2:c.79C>T
NM_001177651.2:c.-56-22C>T
NM_001330652.2:c.-56-22C>T
NM_001379110.1:c.-56-22C>TMANE SELECT
NM_001400909.1:c.-35-43C>T
NM_001400910.1:c.-56-22C>T
NM_001400911.1:c.-56-22C>T
NM_001400912.1:c.-56-22C>T
NM_001400913.1:c.-56-22C>T
NM_006359.3:c.79C>T
NP_001036002.1:p.Pro27Ser
NP_006350.1:p.Pro27Ser
NC_000023.10:g.135067740C>T

Protein change:

P27S

Molecular consequence:

NM_001177651.2:c.-56-22C>T - intron variant - [Sequence Ontology: SO:0001627]
NM_001330652.2:c.-56-22C>T - intron variant - [Sequence Ontology: SO:0001627]
NM_001379110.1:c.-56-22C>T - intron variant - [Sequence Ontology: SO:0001627]
NM_001400909.1:c.-35-43C>T - intron variant - [Sequence Ontology: SO:0001627]
NM_001400910.1:c.-56-22C>T - intron variant - [Sequence Ontology: SO:0001627]
NM_001400911.1:c.-56-22C>T - intron variant - [Sequence Ontology: SO:0001627]
NM_001400912.1:c.-56-22C>T - intron variant - [Sequence Ontology: SO:0001627]
NM_001400913.1:c.-56-22C>T - intron variant - [Sequence Ontology: SO:0001627]
NM_001042537.2:c.79C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_006359.3:c.79C>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

Recent activity

Clear Turn Off Turn On

TMED9 [Ursus arctos]
TMED9 [Ursus arctos]
Gene ID:113261588

Gene

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
SCV004487149	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Dec 17, 2022)	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

SCV004487149

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Dec 17, 2022)

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, SCV004487149.1

#	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. Algorithms developed to predict the effect of missense changes on protein structure and function output the following: SIFT: "Tolerated"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0". The serine amino acid residue is found in multiple mammalian species, which suggests that this missense change does not adversely affect protein function. This variant has not been reported in the literature in individuals affected with SLC9A6-related conditions. This variant is present in population databases (rs782655120, gnomAD 0.003%). This sequence change replaces proline, which is neutral and non-polar, with serine, which is neutral and polar, at codon 27 of the SLC9A6 protein (p.Pro27Ser).

#	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