NM_001379110.1(SLC9A6):c.1832C>T (p.Thr611Ile) AND Christianson syndrome

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jul 28, 2019
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:: RCV001237236.7

Allele description [Variation Report for NM_001379110.1(SLC9A6):c.1832C>T (p.Thr611Ile)]

NM_001379110.1(SLC9A6):c.1832C>T (p.Thr611Ile)

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.1832C>T (p.Thr611Ile)

HGVS:

NC_000023.11:g.136044516C>T
NG_017160.1:g.64090C>T
NM_001042537.2:c.1898C>T
NM_001177651.2:c.1742C>T
NM_001330652.2:c.1646C>T
NM_001379110.1:c.1832C>TMANE SELECT
NM_006359.3:c.1802C>T
NP_001036002.1:p.Thr633Ile
NP_001171122.1:p.Thr581Ile
NP_001317581.1:p.Thr549Ile
NP_001366039.1:p.Thr611Ile
NP_006350.1:p.Thr601Ile
NC_000023.10:g.135126675C>T
NM_006359.2:c.1802C>T

Protein change:

T549I

Links:

dbSNP: rs2071564662

NCBI 1000 Genomes Browser:

rs2071564662

Molecular consequence:

NM_001042537.2:c.1898C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001177651.2:c.1742C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001330652.2:c.1646C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001379110.1:c.1832C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_006359.3:c.1802C>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
SCV001409989	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Jul 28, 2019)	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

SCV001409989

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Jul 28, 2019)

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):240-242.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Invitae, SCV001409989.5

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

Description

Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be tolerated, but these predictions have not been confirmed by published functional studies and their clinical significance is uncertain. 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. This variant is not present in population databases (ExAC no frequency). This sequence change replaces threonine with isoleucine at codon 601 of the SLC9A6 protein (p.Thr601Ile). The threonine residue is moderately conserved and there is a moderate physicochemical difference between threonine and isoleucine.

#	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: Feb 28, 2024

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