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NM_001042432.2(CLN3):c.175G>A (p.Ala59Thr) AND not provided

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
Nov 3, 2022
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:
RCV002462842.1

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)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002756999GeneDx
criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)		Likely pathogenic
(Nov 3, 2022) 		germlineclinical testing

Citation Link

Help

Summary from all submissions

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

Details of each submission

From GeneDx, SCV002756999.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

Published functional studies demonstrate that the variant causes altered splicing of the CLN3 pre-mRNA, protein expression, cell histology, and SCMAS expression (Zhang et al., 2021); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Not observed at significant frequency in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 27104957, 29753273, 33507216, 32441891, 33497524, 30446867)

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

Last Updated: Oct 26, 2024