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NM_004937.3(CTNS):c.270A>T (p.Thr90=) AND multiple conditions

Germline classification:
Likely benign (1 submission)
Last evaluated:
Jan 29, 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:
RCV002542886.9

Allele description [Variation Report for NM_004937.3(CTNS):c.270A>T (p.Thr90=)]

NM_004937.3(CTNS):c.270A>T (p.Thr90=)

Genes:
CTNS-AS1:CTNS antisense RNA 1 [Gene - HGNC]
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.270A>T (p.Thr90=)
HGVS:
  • NC_000017.11:g.3655042A>T
  • NG_012489.2:g.23575A>T
  • NM_001031681.3:c.270A>T
  • NM_001374492.1:c.270A>T
  • NM_001374493.1:c.-172A>T
  • NM_001374494.1:c.-172A>T
  • NM_001374495.1:c.-172A>T
  • NM_001374496.1:c.-172A>T
  • NM_004937.3:c.270A>TMANE SELECT
  • NP_001026851.2:p.Thr90=
  • NP_001361421.1:p.Thr90=
  • NP_004928.2:p.Thr90=
  • NC_000017.10:g.3558336A>T
  • NG_012489.1:g.23575A>T
Links:
dbSNP: rs754247532
NCBI 1000 Genomes Browser:
rs754247532
Molecular consequence:
  • NM_001374493.1:c.-172A>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001374494.1:c.-172A>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001374495.1:c.-172A>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001374496.1:c.-172A>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001031681.3:c.270A>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001374492.1:c.270A>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_004937.3:c.270A>T - synonymous variant - [Sequence Ontology: SO:0001819]

Condition(s)

Name:
Ocular cystinosis
Synonyms:
Cystinosis, ocular nonnephropathic; Cystinosis, adult, nonnephropathic; Cystinosis, benign, nonnephropathic
Identifiers:
MONDO: MONDO:0009064; MedGen: C2931013; Orphanet: 213; OMIM: 219750
Name:
Juvenile nephropathic cystinosis
Synonyms:
CYSTINOSIS, LATE-ONSET JUVENILE OR ADOLESCENT NEPHROPATHIC TYPE
Identifiers:
MONDO: MONDO:0009066; MedGen: C0268626; Orphanet: 213; Orphanet: 411634; OMIM: 219900
Name:
Inborn genetic diseases
Identifiers:
MeSH: D030342; MedGen: C0950123

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV001686822Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))
Likely benign
(Jan 29, 2024)
germlineclinical testing

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

Summary from all submissions

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

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From Invitae, SCV001686822.4

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

Last Updated: Jul 15, 2024