NM_017882.3(CLN6):c.486+1G>A AND Seizures

Clinical significance:Likely pathogenic (Last evaluated: Nov 2, 2016)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:
current
Accession:
RCV000719064.1

Allele description [Variation Report for NM_017882.3(CLN6):c.486+1G>A]

NM_017882.3(CLN6):c.486+1G>A

Gene:
CLN6:CLN6 transmembrane ER protein [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
15q23
Genomic location:
Preferred name:
NM_017882.3(CLN6):c.486+1G>A
HGVS:
  • NC_000015.10:g.68211674C>T
  • NG_008764.2:g.50538G>A
  • NM_017882.3:c.486+1G>AMANE SELECT
  • LRG_832t1:c.486+1G>A
  • LRG_832:g.50538G>A
  • NC_000015.9:g.68504012C>T
  • NM_017882.2:c.486+1G>A
Links:
dbSNP: rs756522171
NCBI 1000 Genomes Browser:
rs756522171
Molecular consequence:
  • NM_017882.3:c.486+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
Observations:
1

Condition(s)

Name:
Seizures
Identifiers:
MedGen: C0036572; Human Phenotype Ontology: HP:0001250

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000849928Ambry Geneticscriteria provided, single submitter
Likely pathogenic
(Nov 2, 2016)
germlineclinical testing

Citation Link

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknown1not providednot provided1not providedclinical testing

Details of each submission

From Ambry Genetics, SCV000849928.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testingnot provided

Description

The c.486+1G>A intronic variant results from a G to A substitution one nucleotide after coding exon 4 of the CLN6 gene. This variant was not reported in population based cohorts in the following databases: Database of Single Nucleotide Polymorphisms (dbSNP), NHLBI Exome Sequencing Project (ESP), and 1000 Genomes Project. In the ESP, this variant was not observed in 6498 samples (12996 alleles) with coverage at this position. This nucleotide position is highly conserved in available vertebrate species. Alterations that disrupt the canonical splice site are expected to cause aberrant splicing, resulting in an abnormal protein or a transcript that is subject to nonsense-mediated mRNA decay. As such, this alteration is classified as likely pathogenic.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknown1not providednot provided1not providednot providednot provided

Last Updated: Jul 29, 2021

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