NM_017882.3(CLN6):c.150C>G (p.Tyr50Ter) AND not provided

Germline classification:: Pathogenic (3 submissions)
Last evaluated:: Nov 15, 2024
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV000058908.20

Allele description [Variation Report for NM_017882.3(CLN6):c.150C>G (p.Tyr50Ter)]

NM_017882.3(CLN6):c.150C>G (p.Tyr50Ter)

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.150C>G (p.Tyr50Ter)

Other names:

Tyyr50X

HGVS:

NC_000015.10:g.68218584G>C
NG_008764.2:g.43628C>G
NM_017882.3:c.150C>GMANE SELECT
NP_060352.1:p.Tyr50Ter
LRG_832t1:c.150C>G
LRG_832:g.43628C>G
LRG_832p1:p.Tyr50Ter
NC_000015.9:g.68510922G>C
NG_008764.1:g.16159C>G
NM_017882.2:c.150C>G

Protein change:

Y50*

Links:

dbSNP: rs154774640

Molecular consequence:

NM_017882.3:c.150C>G - nonsense - [Sequence Ontology: SO:0001587]

Observations:

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000090429	SNPedia	no classification provided	not provided	germline	not provided	PubMed (1) [See all records that cite this PMID]
SCV000568366	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Pathogenic (Nov 15, 2024)	germline	clinical testing	Citation Link,
SCV004703339	CeGaT Center for Human Genetics Tuebingen	criteria provided, single submitter (CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)	Pathogenic (Jan 1, 2024)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000090429

SNPedia

no classification provided

not provided

germline

not provided

PubMed (1)
[See all records that cite this PMID]

SCV000568366

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Pathogenic
(Nov 15, 2024)

germline

clinical testing

Citation Link,

SCV004703339

CeGaT Center for Human Genetics Tuebingen

criteria provided, single submitter

(CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)

Pathogenic
(Jan 1, 2024)

germline

clinical testing

Citation Link

Description

Kufs Type A disease: SCV000090429

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	1	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	not provided	not provided	not provided	not provided	1	not provided	literature only

Citations

PubMed

Kufs disease, the major adult form of neuronal ceroid lipofuscinosis, caused by mutations in CLN6.

Arsov T, Smith KR, Damiano J, Franceschetti S, Canafoglia L, Bromhead CJ, Andermann E, Vears DF, Cossette P, Rajagopalan S, McDougall A, Sofia V, Farrell M, Aguglia U, Zini A, Meletti S, Morbin M, Mullen S, Andermann F, Mole SE, Bahlo M, Berkovic SF.

Am J Hum Genet. 2011 May 13;88(5):566-73. doi: 10.1016/j.ajhg.2011.04.004. Epub 2011 May 5.

PubMed [citation]

PMID:: 21549341
PMCID:: PMC3146726

Details of each submission

From SNPedia, SCV000090429.1

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

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

From GeneDx, SCV000568366.5

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

Description

Reported previously in a patient with a clinical diagnosis of Kufs disease who was also heterozygous for two missense substitutions in the CLN6 gene, although no further clinical details were provided and parental testing was not performed to determine the phase of the three variants (PMID: 21549341); Reported previously as a pathogenic variant in a cohort of patients referred for epilepsy genetic testing; however, no specific clinical information was provided (PMID: 31440721); Nonsense variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss of function is a known mechanism of disease; Not observed at significant frequency in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 31980526, 31440721, 26075876, 33024953, 21549341)

#	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

From CeGaT Center for Human Genetics Tuebingen, SCV004703339.18

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

Description

CLN6: PVS1, PM2, PM3

#	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		1	not provided	not provided	not provided

Last Updated: Apr 4, 2026

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