NM_001042432.2(CLN3):c.748C>T (p.Arg250Trp) 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:: RCV001119056.6

Allele description [Variation Report for NM_001042432.2(CLN3):c.748C>T (p.Arg250Trp)]

NM_001042432.2(CLN3):c.748C>T (p.Arg250Trp)

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.748C>T (p.Arg250Trp)

HGVS:

NC_000016.10:g.28484048G>A
NG_008654.2:g.13255C>T
NM_000086.2:c.748C>T
NM_001042432.2:c.748C>TMANE SELECT
NM_001286104.2:c.676C>T
NM_001286105.2:c.448C>T
NM_001286109.2:c.514C>T
NM_001286110.2:c.586C>T
NP_000077.1:p.Arg250Trp
NP_001035897.1:p.Arg250Trp
NP_001035897.1:p.Arg250Trp
NP_001273033.1:p.Arg226Trp
NP_001273034.1:p.Arg150Trp
NP_001273038.1:p.Arg172Trp
NP_001273039.1:p.Arg196Trp
LRG_689t1:c.748C>T
LRG_689t2:c.748C>T
LRG_689:g.13255C>T
LRG_689p1:p.Arg250Trp
LRG_689p2:p.Arg250Trp
NC_000016.9:g.28495369G>A
NM_001042432.1:c.748C>T
NM_001042432.2:c.748C>T

Protein change:

R150W

Links:

dbSNP: rs764881080

NCBI 1000 Genomes Browser:

rs764881080

Molecular consequence:

NM_000086.2:c.748C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001042432.2:c.748C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001286104.2:c.676C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001286105.2:c.448C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001286109.2:c.514C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001286110.2:c.586C>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
SCV001277396	Illumina Laboratory Services, Illumina	criteria provided, single submitter (ICSL Variant Classification Criteria 13 December 2019)	Uncertain significance (Apr 28, 2017)	germline	clinical testing	Citation Link,
SCV002027112	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

SCV001277396

Illumina Laboratory Services, Illumina

criteria provided, single submitter

(ICSL Variant Classification Criteria 13 December 2019)

Uncertain significance
(Apr 28, 2017)

germline

clinical testing

Citation Link,

SCV002027112

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	germline	unknown	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 Illumina Laboratory Services, Illumina, SCV001277396.1

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

Description

This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases did not allow this variant to be ruled in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance.

#	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
2	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Genome-Nilou Lab, SCV002027112.1

#	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: Sep 29, 2024

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