NM_001042432.2(CLN3):c.1256G>A (p.Gly419Glu) 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:: RCV000673887.3

Allele description [Variation Report for NM_001042432.2(CLN3):c.1256G>A (p.Gly419Glu)]

NM_001042432.2(CLN3):c.1256G>A (p.Gly419Glu)

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.1256G>A (p.Gly419Glu)

HGVS:

NC_000016.10:g.28477577C>T
NG_008654.2:g.19726G>A
NM_000086.2:c.1256G>A
NM_001042432.2:c.1256G>AMANE SELECT
NM_001286104.2:c.1184G>A
NM_001286105.2:c.956G>A
NM_001286109.2:c.1022G>A
NM_001286110.2:c.1094G>A
NP_000077.1:p.Gly419Glu
NP_001035897.1:p.Gly419Glu
NP_001035897.1:p.Gly419Glu
NP_001273033.1:p.Gly395Glu
NP_001273034.1:p.Gly319Glu
NP_001273038.1:p.Gly341Glu
NP_001273039.1:p.Gly365Glu
LRG_689t1:c.1256G>A
LRG_689t2:c.1256G>A
LRG_689:g.19726G>A
LRG_689p1:p.Gly419Glu
LRG_689p2:p.Gly419Glu
NC_000016.9:g.28488898C>T
NM_001042432.1:c.1256G>A
NM_001042432.2:c.1256G>A

Protein change:

G319E

Links:

dbSNP: rs796052338

NCBI 1000 Genomes Browser:

rs796052338

Molecular consequence:

NM_000086.2:c.1256G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001042432.2:c.1256G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001286104.2:c.1184G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001286105.2:c.956G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001286109.2:c.1022G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001286110.2:c.1094G>A - 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
SCV000799140	Counsyl	criteria provided, single submitter (Counsyl Autosomal Recessive and X-Linked Classification Criteria (2018))	Uncertain significance (Apr 11, 2018)	unknown	clinical testing	PubMed (1) [See all records that cite this PMID] Citation Link,
SCV002027083	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

SCV000799140

Counsyl

criteria provided, single submitter

(Counsyl Autosomal Recessive and X-Linked Classification Criteria (2018))

Uncertain significance
(Apr 11, 2018)

unknown

clinical testing

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

Citation Link,

SCV002027083

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	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Clinical application of whole-exome sequencing across clinical indications.

Retterer K, Juusola J, Cho MT, Vitazka P, Millan F, Gibellini F, Vertino-Bell A, Smaoui N, Neidich J, Monaghan KG, McKnight D, Bai R, Suchy S, Friedman B, Tahiliani J, Pineda-Alvarez D, Richard G, Brandt T, Haverfield E, Chung WK, Bale S.

Genet Med. 2016 Jul;18(7):696-704. doi: 10.1038/gim.2015.148. Epub 2015 Dec 3.

PubMed [citation]

PMID:: 26633542

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 Counsyl, SCV000799140.1

#	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

From Genome-Nilou Lab, SCV002027083.1

#	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: Mar 5, 2024

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