NM_017882.3(CLN6):c.486+2T>C AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Oct 18, 2013
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:: RCV000187099.1

Allele description [Variation Report for NM_017882.3(CLN6):c.486+2T>C]

NM_017882.3(CLN6):c.486+2T>C

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+2T>C

HGVS:

NC_000015.10:g.68211673A>G
NG_008764.2:g.50539T>C
NG_131414.1:g.576A>G
NM_001411068.1:c.582+2T>C
NM_017882.3:c.486+2T>CMANE SELECT
LRG_832t1:c.486+2T>C
LRG_832:g.50539T>C
NC_000015.9:g.68504011A>G
NM_017882.2:c.486+2T>C

Links:

dbSNP: rs796052355

NCBI 1000 Genomes Browser:

rs796052355

Molecular consequence:

NM_001411068.1:c.582+2T>C - splice donor variant - [Sequence Ontology: SO:0001575]
NM_017882.3:c.486+2T>C - splice donor variant - [Sequence Ontology: SO:0001575]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: CN517202

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000240674	GeneDx	criteria provided, single submitter (GeneDx Variant Classification (06012015))	Pathogenic (Oct 18, 2013)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000240674

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification (06012015))

Pathogenic
(Oct 18, 2013)

germline

clinical testing

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing

Details of each submission

From GeneDx, SCV000240674.11

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

Description

c.486+2 T>C: IVS4+2 T>C in intron 4 of the CLN6 gene (NM_017882.2). The c.486+2 T>C splice site mutation in CLN6 destroys the canonical splice donor site in intron 4. 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. Although this mutation has not been reported previously to our knowledge, it is expected to be a pathogenic mutation. The variant is found in CHILD-EPI panel(s).

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

Last Updated: Jun 10, 2023

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