NM_001042432.2(CLN3):c.206C>T (p.Ser69Leu) AND Neuronal ceroid lipofuscinosis 3

Germline classification:: Uncertain significance (2 submissions)
Last evaluated:: Sep 5, 2021
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:: RCV001330764.10

Allele description [Variation Report for NM_001042432.2(CLN3):c.206C>T (p.Ser69Leu)]

NM_001042432.2(CLN3):c.206C>T (p.Ser69Leu)

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.206C>T (p.Ser69Leu)

Other names:

p.S69L:TCG>TTG

HGVS:

NC_000016.10:g.28489306G>A
NG_008654.2:g.7997C>T
NM_000086.2:c.206C>T
NM_001042432.2:c.206C>TMANE SELECT
NM_001286104.2:c.206C>T
NM_001286105.2:c.-15C>T
NM_001286109.2:c.44C>T
NM_001286110.2:c.44C>T
NP_000077.1:p.Ser69Leu
NP_001035897.1:p.Ser69Leu
NP_001035897.1:p.Ser69Leu
NP_001273033.1:p.Ser69Leu
NP_001273038.1:p.Ser15Leu
NP_001273039.1:p.Ser15Leu
LRG_689t1:c.206C>T
LRG_689t2:c.206C>T
LRG_689:g.7997C>T
LRG_689p1:p.Ser69Leu
LRG_689p2:p.Ser69Leu
NC_000016.9:g.28500627G>A
NM_001042432.1:c.206C>T
NM_001042432.2:c.206C>T
p.Ser69Leu

Protein change:

S15L

Links:

dbSNP: rs769840061

NCBI 1000 Genomes Browser:

rs769840061

Molecular consequence:

NM_001286105.2:c.-15C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_000086.2:c.206C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001042432.2:c.206C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001286104.2:c.206C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001286109.2:c.44C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001286110.2:c.44C>T - missense variant - [Sequence Ontology: SO:0001583]

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
SCV001522554	Baylor Genetics	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (Jul 8, 2020)	unknown	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV002027137	Genome-Nilou Lab	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (Sep 5, 2021)	germline	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

SCV001522554

Baylor Genetics

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance
(Jul 8, 2020)

unknown

clinical testing

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

SCV002027137

Genome-Nilou Lab

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance
(Sep 5, 2021)

germline

clinical testing

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	no	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	unknown	yes	not provided	not provided	not provided	not provided	not provided	clinical testing

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 Baylor Genetics, SCV001522554.1

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

Description

This variant was determined to be of uncertain significance according to ACMG Guidelines, 2015 [PMID:25741868].

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

From Genome-Nilou Lab, SCV002027137.1

#	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	germline	no	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Nov 3, 2024

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