NM_001042432.2(CLN3):c.1056+1G>A AND Neuronal ceroid lipofuscinosis

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: Jan 11, 2024
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:: RCV003534072.2

Allele description [Variation Report for NM_001042432.2(CLN3):c.1056+1G>A]

NM_001042432.2(CLN3):c.1056+1G>A

Gene:

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

Variant type:

single nucleotide variant

Cytogenetic location:

16p12.1

Genomic location:

Preferred name:

NM_001042432.2(CLN3):c.1056+1G>A

HGVS:

NC_000016.10:g.28482104C>T
NG_008654.2:g.15199G>A
NM_000086.2:c.1056+1G>A
NM_001042432.2:c.1056+1G>AMANE SELECT
NM_001286104.2:c.984+1G>A
NM_001286105.2:c.756+1G>A
NM_001286109.2:c.822+1G>A
NM_001286110.2:c.894+1G>A
LRG_689t1:c.1056+1G>A
LRG_689:g.15199G>A
NC_000016.9:g.28493425C>T

Molecular consequence:

NM_000086.2:c.1056+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001042432.2:c.1056+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001286104.2:c.984+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001286105.2:c.756+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001286109.2:c.822+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001286110.2:c.894+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]

Condition(s)

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

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Lrrc30 leucine rich repeat containing 30 [Mus musculus]
Lrrc30 leucine rich repeat containing 30 [Mus musculus]
Gene ID:240131

Gene
240131[uid] AND (alive[prop]) (1)
Gene
Arr3p [Saccharomyces cerevisiae YJM981]
Arr3p [Saccharomyces cerevisiae YJM981]
gi|768899213|gnl|McCuskerlabDuke|H7 M981P00331|gb|AJW27273.1|

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004259877	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Likely pathogenic (Jan 11, 2024)	germline	clinical testing	PubMed (4) [See all records that cite these PMIDs] 16199547, 9311735, 28542676, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004259877

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Likely pathogenic
(Jan 11, 2024)

germline

clinical testing

PubMed (4)
[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

Splicing in action: assessing disease causing sequence changes.

Baralle D, Baralle M.

J Med Genet. 2005 Oct;42(10):737-48. Review.

PubMed [citation]

PMID:: 16199547
PMCID:: PMC1735933

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

See all PubMed Citations (4)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV004259877.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (4)

Description

This sequence change affects a donor splice site in intron 14 of the CLN3 gene. It is expected to disrupt RNA splicing. Variants that disrupt the donor or acceptor splice site typically lead to a loss of protein function (PMID: 16199547), and loss-of-function variants in CLN3 are known to be pathogenic (PMID: 9311735, 28542676). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with CLN3-related conditions. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic.

#	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: Sep 29, 2024

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