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NM_001042432.2(CLN3):c.175G>A (p.Ala59Thr) AND Neuronal ceroid lipofuscinosis 3

Germline classification:
Likely pathogenic (2 submissions)
Last evaluated:
Mar 3, 2024
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:
RCV001810499.7

Allele description [Variation Report for NM_001042432.2(CLN3):c.175G>A (p.Ala59Thr)]

NM_001042432.2(CLN3):c.175G>A (p.Ala59Thr)

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.175G>A (p.Ala59Thr)
HGVS:
  • NC_000016.10:g.28489337C>T
  • NG_008654.2:g.7966G>A
  • NM_000086.2:c.175G>A
  • NM_001042432.2:c.175G>AMANE SELECT
  • NM_001286104.2:c.175G>A
  • NM_001286105.2:c.-46G>A
  • NM_001286109.2:c.13G>A
  • NM_001286110.2:c.13G>A
  • NP_000077.1:p.Ala59Thr
  • NP_001035897.1:p.Ala59Thr
  • NP_001273033.1:p.Ala59Thr
  • NP_001273038.1:p.Ala5Thr
  • NP_001273039.1:p.Ala5Thr
  • LRG_689t1:c.175G>A
  • LRG_689t2:c.175G>A
  • LRG_689:g.7966G>A
  • LRG_689p1:p.Ala59Thr
  • NC_000016.9:g.28500658C>T
  • NM_001042432.1:c.175G>A
  • NM_001042432.2:c.175G>A
Protein change:
A59T
Links:
dbSNP: rs765893479
NCBI 1000 Genomes Browser:
rs765893479
Molecular consequence:
  • NM_001286105.2:c.-46G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_000086.2:c.175G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001042432.2:c.175G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001286104.2:c.175G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001286109.2:c.13G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001286110.2:c.13G>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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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV004214303Baylor Genetics
criteria provided, single submitter

(ACMG Guidelines, 2015)		Likely pathogenic
(Mar 3, 2024) 		unknownclinical testing

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

Help

Summary from all submissions

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

Citations

PubMed

Clinical and molecular characterization of non-syndromic retinal dystrophy due to c.175G>A mutation in ceroid lipofuscinosis neuronal 3 (CLN3).

Chen FK, Zhang X, Eintracht J, Zhang D, Arunachalam S, Thompson JA, Chelva E, Mallon D, Chen SC, McLaren T, Lamey T, De Roach J, McLenachan S.

Doc Ophthalmol. 2019 Feb;138(1):55-70. doi: 10.1007/s10633-018-9665-7. Epub 2018 Nov 16.

PubMed [citation]
PMID:
30446867

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 Myriad Genetics, Inc., SCV002060092.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

NM_001042432.1(CLN3):c.175G>A(A59T) is a missense variant classified as a variant of uncertain significance in the context of CLN3-related neuronal ceroid lipofuscinosis. A59T has been observed in cases with relevant disease (PMID: 30446867). Functional assessments of this variant are available in the literature (PMID: 30446867). A59T has been observed in population frequency databases (gnomAD: AFR <0.004%). In summary, there is insufficient evidence to classify NM_001042432.1(CLN3):c.175G>A(A59T) as pathogenic or benign. Please note: this variant was assessed in the context of healthy population screening.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownunknownnot providednot providednot providednot providednot providednot providednot provided

From Baylor Genetics, SCV004214303.2

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

Flagged submissions

Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002060092Myriad Genetics, Inc.
flagged submission
Reason: Outlier claim with insufficient supporting evidence
Notes: None

(Myriad Women's Health Autosomal Recessive and X-Linked Classification Criteria (2021))		Uncertain significance
(Nov 3, 2021) 		unknownclinical testing

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

Citation Link

Last Updated: Oct 26, 2024