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NM_006493.4(CLN5):c.486C>T (p.Gly162=) AND CLN5-related disorder

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Dec 5, 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:
RCV003411640.4

Allele description [Variation Report for NM_006493.4(CLN5):c.486C>T (p.Gly162=)]

NM_006493.4(CLN5):c.486C>T (p.Gly162=)

Gene:
CLN5:CLN5 intracellular trafficking protein [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
13q22.3
Genomic location:
Preferred name:
NM_006493.4(CLN5):c.486C>T (p.Gly162=)
HGVS:
  • NC_000013.11:g.76996048C>T
  • NG_009064.1:g.9125C>T
  • NM_001366624.2:c.486C>T
  • NM_006493.4:c.486C>TMANE SELECT
  • NP_001353553.1:p.Gly162=
  • NP_006484.2:p.Gly162=
  • LRG_692t1:c.633C>T
  • LRG_692:g.9125C>T
  • NC_000013.10:g.77570183C>T
  • NM_006493.2:c.633C>T
Links:
dbSNP: rs769007858
NCBI 1000 Genomes Browser:
rs769007858
Molecular consequence:
  • NM_001366624.2:c.486C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_006493.4:c.486C>T - synonymous variant - [Sequence Ontology: SO:0001819]

Condition(s)

Name:
CLN5-related disorder
Synonyms:
CLN5-related condition
Identifiers:

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV004113129PreventionGenetics, part of Exact Sciences
criteria provided, single submitter

(ACMG Guidelines, 2015)		Uncertain significance
(Dec 5, 2022) 		germlineclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical 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 PreventionGenetics, part of Exact Sciences, SCV004113129.1

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

Description

The CLN5 c.633C>T variant is not predicted to result in an amino acid change (p.=). To our knowledge, this variant has not been reported in the literature. This variant is reported in 0.0058% of alleles in individuals of Latino descent in gnomAD (http://gnomad.broadinstitute.org/variant/13-77570183-C-T). Although this variant is silent and is not predicted to change amino acid sequence, splicing prediction software predicts low chance of creating new splice site. This variant is reported in ClinVar as variant of uncertain significance. At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence.

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

Last Updated: Sep 29, 2024