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NM_004937.3(CTNS):c.425_427del (p.Phe142del) AND multiple conditions

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Apr 20, 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:
RCV005091933.1

Allele description [Variation Report for NM_004937.3(CTNS):c.425_427del (p.Phe142del)]

NM_004937.3(CTNS):c.425_427del (p.Phe142del)

Genes:
CTNS-AS1:CTNS antisense RNA 1 [Gene - HGNC]
CTNS:cystinosin, lysosomal cystine transporter [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
17p13.2
Genomic location:
Preferred name:
NM_004937.3(CTNS):c.425_427del (p.Phe142del)
HGVS:
  • NC_000017.11:g.3655316_3655318del
  • NG_012489.2:g.23849_23851del
  • NM_001031681.3:c.425_427del
  • NM_001374492.1:c.425_427del
  • NM_001374493.1:c.-17_-15del
  • NM_001374494.1:c.-17_-15del
  • NM_001374495.1:c.-17_-15del
  • NM_001374496.1:c.-17_-15del
  • NM_004937.3:c.425_427delMANE SELECT
  • NP_001026851.2:p.Phe142del
  • NP_001361421.1:p.Phe142del
  • NP_004928.2:p.Phe142del
  • NC_000017.10:g.3558610_3558612del
  • NM_004937.2:c.425_427delTCT
Protein change:
F142del
Links:
dbSNP: rs1178364162
NCBI 1000 Genomes Browser:
rs1178364162
Molecular consequence:
  • NM_001374493.1:c.-17_-15del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001374494.1:c.-17_-15del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001374495.1:c.-17_-15del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001374496.1:c.-17_-15del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001031681.3:c.425_427del - inframe_deletion - [Sequence Ontology: SO:0001822]
  • NM_001374492.1:c.425_427del - inframe_deletion - [Sequence Ontology: SO:0001822]
  • NM_004937.3:c.425_427del - inframe_deletion - [Sequence Ontology: SO:0001822]

Condition(s)

Name:
Ocular cystinosis
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:
Nephropathic cystinosis (CTNS)
Synonyms:
CYSTINOSIN, DEFECT OF; LYSOSOMAL CYSTINE TRANSPORT PROTEIN, DEFECT OF; Abderhalden Lignac Kaufmann disease; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0100151; MedGen: C2931187; Orphanet: 213; Orphanet: 411629; OMIM: 219800

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002788120Fulgent Genetics, Fulgent Genetics
criteria provided, single submitter

(ACMG Guidelines, 2015)		Uncertain significance
(Apr 20, 2022) 		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

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 Fulgent Genetics, Fulgent Genetics, SCV002788120.1

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

Last Updated: Jul 5, 2025