NM_001042432.2(CLN3):c.985_988del (p.Gly329fs) AND Neuronal ceroid lipofuscinosis

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Dec 14, 2020
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:: RCV001938804.3

Allele description [Variation Report for NM_001042432.2(CLN3):c.985_988del (p.Gly329fs)]

NM_001042432.2(CLN3):c.985_988del (p.Gly329fs)

Gene:

CLN3:CLN3 lysosomal/endosomal transmembrane protein, battenin [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

16p12.1

Genomic location:

Preferred name:

NM_001042432.2(CLN3):c.985_988del (p.Gly329fs)

HGVS:

NC_000016.10:g.28482173_28482176del
NG_008654.2:g.15127_15130del
NM_000086.2:c.985_988del
NM_001042432.2:c.985_988delMANE SELECT
NM_001286104.2:c.913_916del
NM_001286105.2:c.685_688del
NM_001286109.2:c.751_754del
NM_001286110.2:c.823_826del
NP_000077.1:p.Gly329fs
NP_001035897.1:p.Gly329fs
NP_001273033.1:p.Gly305fs
NP_001273034.1:p.Gly229fs
NP_001273038.1:p.Gly251fs
NP_001273039.1:p.Gly275fs
LRG_689t1:c.985_988del
LRG_689:g.15127_15130del
LRG_689p1:p.Gly329fs
NC_000016.9:g.28493494_28493497del

Protein change:

G229fs

Links:

dbSNP: rs2141702839

NCBI 1000 Genomes Browser:

rs2141702839

Molecular consequence:

NM_000086.2:c.985_988del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001042432.2:c.985_988del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001286104.2:c.913_916del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001286105.2:c.685_688del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001286109.2:c.751_754del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001286110.2:c.823_826del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Name:: Neuronal ceroid lipofuscinosis
Synonyms:: Ceroid storage disease
Identifiers:: MONDO: MONDO:0016295; MedGen: C0027877; Orphanet: 79263; OMIM: PS256730

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002205372	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Dec 14, 2020)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 9311735, 28542676, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002205372

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Dec 14, 2020)

germline

clinical testing

PubMed (3)
[See all records that cite these PMIDs]

Help

Summary from all submissions

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

Citations

PubMed

Spectrum of mutations in the Batten disease gene, CLN3.

Munroe PB, Mitchison HM, O'Rawe AM, Anderson JW, Boustany RM, Lerner TJ, Taschner PE, de Vos N, Breuning MH, Gardiner RM, Mole SE.

Am J Hum Genet. 1997 Aug;61(2):310-6.

PubMed [citation]

PMID:: 9311735
PMCID:: PMC1715900

Detailed Clinical Phenotype and Molecular Genetic Findings in CLN3-Associated Isolated Retinal Degeneration.

Ku CA, Hull S, Arno G, Vincent A, Carss K, Kayton R, Weeks D, Anderson GW, Geraets R, Parker C, Pearce DA, Michaelides M, MacLaren RE, Robson AG, Holder GE, Heon E, Raymond FL, Moore AT, Webster AR, Pennesi ME.

JAMA Ophthalmol. 2017 Jul 1;135(7):749-760. doi: 10.1001/jamaophthalmol.2017.1401.

PubMed [citation]

PMID:: 28542676
PMCID:: PMC5710208

See all PubMed Citations (3)

Details of each submission

From Invitae, SCV002205372.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (3)

Description

For these reasons, this variant has been classified as Pathogenic. This variant has not been reported in the literature in individuals with CLN3-related conditions. This variant is not present in population databases (ExAC no frequency). This sequence change creates a premature translational stop signal (p.Gly329Serfs*47) in the CLN3 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in CLN3 are known to be pathogenic (PMID: 9311735, 28542676).

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

Last Updated: Feb 28, 2024

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