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NM_005629.4(SLC6A8):c.263-1G>A AND not provided

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Nov 13, 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:
RCV000521906.1

Allele description [Variation Report for NM_005629.4(SLC6A8):c.263-1G>A]

NM_005629.4(SLC6A8):c.263-1G>A

Gene:
SLC6A8:solute carrier family 6 member 8 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
Xq28
Genomic location:
Preferred name:
NM_005629.4(SLC6A8):c.263-1G>A
HGVS:
  • NC_000023.11:g.153690374G>A
  • NG_012016.2:g.7078G>A
  • NM_001142805.2:c.263-1G>A
  • NM_001142806.1:c.-83-1G>A
  • NM_005629.4:c.263-1G>AMANE SELECT
  • NC_000023.10:g.152955829G>A
  • NM_005629.3:c.263-1G>A
Links:
dbSNP: rs1557044165
NCBI 1000 Genomes Browser:
rs1557044165
Molecular consequence:
  • NM_001142805.2:c.263-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001142806.1:c.-83-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_005629.4:c.263-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: CN517202

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000620663GeneDx
criteria provided, single submitter

(GeneDx Variant Classification (06012015))		Pathogenic
(Nov 13, 2018) 		germlineclinical testing

Citation Link

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Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyesnot providednot providednot providednot providednot providedclinical testing

Details of each submission

From GeneDx, SCV000620663.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

The c.263-1G>A variant in the SLC6A8 gene has not been reported previously as a pathogenic variant nor as a benign variant, to our knowledge. It was identified as a de novo variant with confirmed parentage in a patient with a neurodevelopmental phenotype who was tested at GeneDx. This splice site variant destroys the canonical splice acceptor site in intron 1. It is predicted to cause abnormal gene splicing, either leading to an abnormal message that is subject to nonsense-mediated mRNA decay, or to an abnormal protein product if the message is used for protein translation. This variant is not observed in large population cohorts (Lek et al., 2016; 1000 Genomes Consortium et al., 2015; Exome Variant Server). We interpret c.263-1G>A as a pathogenic variant.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Jun 10, 2023