NM_001379110.1(SLC9A6):c.71_88del (p.Ile24_Leu29del) AND Christianson syndrome

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jul 26, 2018
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:: RCV000808896.6

Allele description [Variation Report for NM_001379110.1(SLC9A6):c.71_88del (p.Ile24_Leu29del)]

NM_001379110.1(SLC9A6):c.71_88del (p.Ile24_Leu29del)

Genes:

LOC130068747:ATAC-STARR-seq lymphoblastoid active region 29988 [Gene]
SLC9A6:solute carrier family 9 member A6 [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

Xq26.3

Genomic location:

Preferred name:

NM_001379110.1(SLC9A6):c.71_88del (p.Ile24_Leu29del)

HGVS:

NC_000023.11:g.135985729_135985746del
NG_017160.1:g.5303_5320del
NM_001042537.2:c.227_244del
NM_001177651.2:c.71_88del
NM_001330652.2:c.71_88del
NM_001379110.1:c.71_88delMANE SELECT
NM_006359.3:c.227_244del
NP_001036002.1:p.Ile76_Leu81del
NP_001171122.1:p.Ile24_Leu29del
NP_001317581.1:p.Ile24_Leu29del
NP_001366039.1:p.Ile24_Leu29del
NP_006350.1:p.Ile76_Leu81del
NC_000023.10:g.135067881_135067898del
NC_000023.10:g.135067888_135067905del
NM_006359.2:c.227_244delTCTTCATCCTGCTGCTCA

Links:

dbSNP: rs1603184929

NCBI 1000 Genomes Browser:

rs1603184929

Molecular consequence:

NM_001042537.2:c.227_244del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001177651.2:c.71_88del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001330652.2:c.71_88del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001379110.1:c.71_88del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_006359.3:c.227_244del - inframe_deletion - [Sequence Ontology: SO:0001822]

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
SCV000949026	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Jul 26, 2018)	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

SCV000949026

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Jul 26, 2018)

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, SCV000949026.3

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

Description

This variant, c.227_244del, results in the deletion of 6 amino acids of the SLC9A6 protein (p.Ile76_Leu81del), but otherwise preserves the integrity of the reading frame. This variant is not present in population databases (ExAC no frequency). This variant has not been reported in the literature in individuals with SLC9A6-related disease. Experimental studies and prediction algorithms are not available for this variant, and the functional significance of the deleted amino acids 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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