NM_001042432.2(CLN3):c.125+5G>A AND Neuronal ceroid lipofuscinosis 3

Germline classification:: Likely pathogenic (2 submissions)
Last evaluated:: May 31, 2023
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:: RCV000049665.2

Allele description [Variation Report for NM_001042432.2(CLN3):c.125+5G>A]

NM_001042432.2(CLN3):c.125+5G>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.125+5G>A

HGVS:

NC_000016.10:g.28491477C>T
NG_008654.2:g.5826G>A
NM_000086.2:c.125+5G>A
NM_001042432.2:c.125+5G>AMANE SELECT
NM_001286104.2:c.125+5G>A
NM_001286105.2:c.-96+237G>A
NM_001286109.2:c.-38+237G>A
NM_001286110.2:c.-38+237G>A
LRG_689t1:c.125+5G>A
LRG_689t2:c.125+5G>A
LRG_689:g.5826G>A
NC_000016.9:g.28502798C>T
NM_001042432.1:c.125+5G>A

Links:

dbSNP: rs386833704

NCBI 1000 Genomes Browser:

rs386833704

Molecular consequence:

NM_000086.2:c.125+5G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001042432.2:c.125+5G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001286104.2:c.125+5G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001286105.2:c.-96+237G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001286109.2:c.-38+237G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001286110.2:c.-38+237G>A - intron variant - [Sequence Ontology: SO:0001627]

Condition(s)

Name:: Neuronal ceroid lipofuscinosis 3 (CLN3)
Synonyms:: Spielmeyer Sjogren disease; CLN3 Disease; CLN3-Related Neuronal Ceroid-Lipofuscinosis
Identifiers:: MONDO: MONDO:0008767; MedGen: C0751383; Orphanet: 228346; OMIM: 204200

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000082072	Juha Muilu Group; Institute for Molecular Medicine Finland (FIMM)	no assertion criteria provided	probable-pathogenic	not provided	not provided	PubMed (1) [See all records that cite this PMID]
SCV004214332	Baylor Genetics	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (May 31, 2023)	unknown	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000082072

Juha Muilu Group; Institute for Molecular Medicine Finland (FIMM)

no assertion criteria provided

probable-pathogenic

not provided

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

SCV004214332

Baylor Genetics

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic
(May 31, 2023)

unknown

clinical testing

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

Description

FinDis database variant: This variant was not found or characterized by our laboratory, data were collected from public sources: see reference: SCV000082072

Help

Summary from all submissions

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

Citations

PubMed

Update of the mutation spectrum and clinical correlations of over 360 mutations in eight genes that underlie the neuronal ceroid lipofuscinoses.

Kousi M, Lehesjoki AE, Mole SE.

Hum Mutat. 2012 Jan;33(1):42-63. doi: 10.1002/humu.21624. Epub 2011 Nov 16. Review.

PubMed [citation]

PMID:: 21990111

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 Juha Muilu Group; Institute for Molecular Medicine Finland (FIMM), SCV000082072.1

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

Description

Converted during submission to Likely pathogenic.

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

From Baylor Genetics, SCV004214332.1

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

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

Last Updated: Sep 29, 2024

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