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NM_004937.3(CTNS):c.1015G>A (p.Gly339Arg) AND CTNS-related disorder

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Sep 23, 2024
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
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:
RCV003904807.2

Allele description [Variation Report for NM_004937.3(CTNS):c.1015G>A (p.Gly339Arg)]

NM_004937.3(CTNS):c.1015G>A (p.Gly339Arg)

Gene:
CTNS:cystinosin, lysosomal cystine transporter [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
17p13.2
Genomic location:
Preferred name:
NM_004937.3(CTNS):c.1015G>A (p.Gly339Arg)
HGVS:
  • NC_000017.11:g.3660280G>A
  • NG_012489.2:g.28813G>A
  • NM_001031681.3:c.1015G>A
  • NM_001374492.1:c.1015G>A
  • NM_001374493.1:c.574G>A
  • NM_001374494.1:c.574G>A
  • NM_001374495.1:c.574G>A
  • NM_001374496.1:c.574G>A
  • NM_004937.3:c.1015G>AMANE SELECT
  • NP_001026851.2:p.Gly339Arg
  • NP_001361421.1:p.Gly339Arg
  • NP_001361422.1:p.Gly192Arg
  • NP_001361423.1:p.Gly192Arg
  • NP_001361424.1:p.Gly192Arg
  • NP_001361425.1:p.Gly192Arg
  • NP_004928.2:p.Gly339Arg
  • NC_000017.10:g.3563574G>A
  • NM_001031681.2:c.1015G>A
  • NM_004937.2:c.1015G>A
  • O60931:p.Gly339Arg
Protein change:
G192R; GLY339ARG
Links:
UniProtKB: O60931#VAR_010695; OMIM: 606272.0015; dbSNP: rs121908127
NCBI 1000 Genomes Browser:
rs121908127
Molecular consequence:
  • NM_001031681.3:c.1015G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001374492.1:c.1015G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001374493.1:c.574G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001374494.1:c.574G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001374495.1:c.574G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001374496.1:c.574G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_004937.3:c.1015G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

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

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV004725984PreventionGenetics, part of Exact Sciences
no assertion criteria provided
Pathogenic
(Sep 23, 2024) 		germlineclinical testing

Help

Summary from all submissions

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

Details of each submission

From PreventionGenetics, part of Exact Sciences, SCV004725984.2

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

Description

The CTNS c.1015G>A variant is predicted to result in the amino acid substitution p.Gly339Arg. This variant has been reported in the homozygous or compound heterozygous state with a second causative CTNS variant in multiple cystinosis patients (Attard et al. 1999. PubMed ID: 10556299; Rupar et al. 2001. PubMed ID: 11565547; Shahkarami et al. 2013. PubMed ID: 23640116; Soliman et al. 2014. PubMed ID: 24464559). The p.Gly339 amino acid is located in the seventh transmembrane domain of the cystinosin protein, and in an in vitro functional study this substitution was reported to abolish cysteine transport (Kalatzis et al. 2004. PubMed ID: 15128704). This variant is reported in 0.0062% of alleles in individuals of European (Non-Finnish) descent in gnomAD. This variant is interpreted as pathogenic.

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

Last Updated: Nov 3, 2024