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

Germline classification:: Uncertain significance (2 submissions)
Last evaluated:: Sep 22, 2023
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV001331523.5

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

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

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>C

HGVS:

NC_000023.11:g.135985527G>C
NG_017160.1:g.5101G>C
NM_001042537.2:c.25G>C
NM_001177651.2:c.-57+50G>C
NM_001330652.2:c.-57+55G>C
NM_001379110.1:c.-57+50G>CMANE SELECT
NM_006359.3:c.25G>C
NP_001036002.1:p.Ala9Pro
NP_006350.1:p.Ala9Pro
NC_000023.10:g.135067686G>C
NM_001042537.1:c.25G>C

Protein change:

A9P

Links:

dbSNP: rs201523857

NCBI 1000 Genomes Browser:

rs201523857

Molecular consequence:

NM_001177651.2:c.-57+50G>C - intron variant - [Sequence Ontology: SO:0001627]
NM_001330652.2:c.-57+55G>C - intron variant - [Sequence Ontology: SO:0001627]
NM_001379110.1:c.-57+50G>C - intron variant - [Sequence Ontology: SO:0001627]
NM_001042537.2:c.25G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_006359.3:c.25G>C - 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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Homo sapiens zinc finger protein 285A, mRNA (cDNA clone IMAGE:30915539), partial...
Homo sapiens zinc finger protein 285A, mRNA (cDNA clone IMAGE:30915539), partial cds
gi|50959891|gb|BC074824.2|

Nucleotide
RecName: Full=Heat shock factor 2-binding protein
RecName: Full=Heat shock factor 2-binding protein
gi|8134485|sp|O75031.1|HSF2B_HUMAN

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001523579	Baylor Genetics	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (Jul 3, 2019)	unknown	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV002201495	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Sep 22, 2023)	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

SCV001523579

Baylor Genetics

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance
(Jul 3, 2019)

unknown

clinical testing

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

SCV002201495

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Sep 22, 2023)

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
not provided	unknown	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

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 Baylor Genetics, SCV001523579.1

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

Description

This variant was determined to be of uncertain significance according to ACMG Guidelines, 2015 [PMID:25741868].

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	unknown	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Labcorp Genetics (formerly Invitae), Labcorp, SCV002201495.3

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

Description

This sequence change replaces alanine, which is neutral and non-polar, with proline, which is neutral and non-polar, at codon 9 of the SLC9A6 protein (p.Ala9Pro). This variant is present in population databases (no rsID available, gnomAD 0.01%). This variant has not been reported in the literature in individuals affected with SLC9A6-related conditions. This missense change has been observed to be homozygous or hemizygous in an individual who did not have the expected clinical features for that genetic result (Invitae). ClinVar contains an entry for this variant (Variation ID: 1030062). Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. 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.

#	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

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