NM_017882.3(CLN6):c.486+8C>T AND Agenesis of the corpus callosum with peripheral neuropathy

Germline classification:: Benign (1 submission)
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:: RCV001258279.10

Allele description [Variation Report for NM_017882.3(CLN6):c.486+8C>T]

NM_017882.3(CLN6):c.486+8C>T

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+8C>T

HGVS:

NC_000015.10:g.68211667G>A
NG_008764.2:g.50545C>T
NM_017882.3:c.486+8C>TMANE SELECT
LRG_832t1:c.486+8C>T
LRG_832:g.50545C>T
NC_000015.9:g.68504005G>A
NM_017882.2:c.486+8C>T

Links:

dbSNP: rs149692285

NCBI 1000 Genomes Browser:

rs149692285

Molecular consequence:

NM_017882.3:c.486+8C>T - intron variant - [Sequence Ontology: SO:0001627]

Condition(s)

Name:: Agenesis of the corpus callosum with peripheral neuropathy (ACCPN)
Synonyms:: Andermann syndrome; Charlevoix disease; Corpus callosum agenesis neuronopathy; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0000902; MedGen: C0795950; Orphanet: 1496; OMIM: 218000

Recent activity

Clear Turn Off Turn On

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

Help

Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001435204	Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard	criteria provided, single submitter (ACMG Guidelines, 2015)	Benign	germline	research	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001435204

Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard

criteria provided, single submitter

(ACMG Guidelines, 2015)

Benign

germline

research

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	yes	not provided	not provided	not provided	not provided	not provided	research

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

Details of each submission

From Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard, SCV001435204.1

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

Description

The heterozygous c.486+8C>T variant in CLN6 has been identified in 3 individuals with neuronal ceroid lipofuscinosis, including 2 individuals with no other variants identified in CLN6 (PMID: 21990111), but has been identified in >2% of European (Finnish) chromosomes and 14 homozygotes by ExAC (http://gnomad.broadinstitue.org/). In summary, this variant meets criteria to be classified as benign for autosomal recessive neuronal ceroid lipofuscinosis.

#	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 29, 2024

ClinVar

Relating variation to medicine