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NM_001042432.2(CLN3):c.597C>A (p.Tyr199Ter) AND Neuronal ceroid lipofuscinosis 3

Germline classification:
Pathogenic/Likely pathogenic (3 submissions)
Last evaluated:
Sep 21, 2023
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:
RCV000169443.5

Allele description [Variation Report for NM_001042432.2(CLN3):c.597C>A (p.Tyr199Ter)]

NM_001042432.2(CLN3):c.597C>A (p.Tyr199Ter)

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.597C>A (p.Tyr199Ter)
HGVS:
  • NC_000016.10:g.28486427G>T
  • NG_008654.2:g.10876C>A
  • NM_000086.2:c.597C>A
  • NM_001042432.2:c.597C>AMANE SELECT
  • NM_001286104.2:c.525C>A
  • NM_001286105.2:c.297C>A
  • NM_001286109.2:c.363C>A
  • NM_001286110.2:c.435C>A
  • NP_000077.1:p.Tyr199Ter
  • NP_001035897.1:p.Tyr199Ter
  • NP_001035897.1:p.Tyr199Ter
  • NP_001273033.1:p.Tyr175Ter
  • NP_001273034.1:p.Tyr99Ter
  • NP_001273038.1:p.Tyr121Ter
  • NP_001273039.1:p.Tyr145Ter
  • LRG_689t1:c.597C>A
  • LRG_689t2:c.597C>A
  • LRG_689:g.10876C>A
  • LRG_689p1:p.Tyr199Ter
  • LRG_689p2:p.Tyr199Ter
  • NC_000016.9:g.28497748G>T
  • NM_000086.2:c.597C>A
  • NM_001042432.1:c.597C>A
Protein change:
Y121*; TYR199TER
Links:
OMIM: 607042.0006; dbSNP: rs267606737
NCBI 1000 Genomes Browser:
rs267606737
Molecular consequence:
  • NM_000086.2:c.597C>A - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001042432.2:c.597C>A - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001286104.2:c.525C>A - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001286105.2:c.297C>A - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001286109.2:c.363C>A - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001286110.2:c.435C>A - nonsense - [Sequence Ontology: SO:0001587]

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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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000220861Counsyl
criteria provided, single submitter

(Counsyl Autosomal and X-linked Recessive Disease Classification criteria (2015))
Likely pathogenic
(Nov 6, 2014)
unknownliterature only

PubMed (3)
[See all records that cite these PMIDs]

Counsyl Autosomal and X-linked Recessive Disease Classification criteria (2015),

Citation Link,

SCV001977446Genome-Nilou Lab
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Aug 10, 2021)
germlineclinical testing

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

SCV004214315Baylor Genetics
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Sep 21, 2023)
unknownclinical testing

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

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlinenonot providednot providednot providednot providednot providedclinical testing
not providedunknownunknownnot providednot providednot providednot providednot providedclinical testing, 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

The juvenile Batten disease protein, CLN3, and its role in regulating anterograde and retrograde post-Golgi trafficking.

Cotman SL, Staropoli JF.

Clin Lipidol. 2012 Feb;7(1):79-91.

PubMed [citation]
PMID:
22545070
PMCID:
PMC3334816
See all PubMed Citations (4)

Details of each submission

From Counsyl, SCV000220861.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedliterature only PubMed (3)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownunknownnot providednot providednot providednot providednot providednot providednot provided

From Genome-Nilou Lab, SCV001977446.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlinenonot providednot providednot providednot providednot providednot providednot provided

From Baylor Genetics, SCV004214315.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Sep 29, 2024