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NM_004937.3(CTNS):c.971-1G>C AND Nephropathic cystinosis

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
Mar 1, 2021
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:
RCV001375476.1

Allele description [Variation Report for NM_004937.3(CTNS):c.971-1G>C]

NM_004937.3(CTNS):c.971-1G>C

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.971-1G>C
HGVS:
  • NC_000017.11:g.3660235G>C
  • NG_012489.2:g.28768G>C
  • NM_001031681.3:c.971-1G>C
  • NM_001374492.1:c.971-1G>C
  • NM_001374493.1:c.530-1G>C
  • NM_001374494.1:c.530-1G>C
  • NM_001374495.1:c.530-1G>C
  • NM_001374496.1:c.530-1G>C
  • NM_004937.3:c.971-1G>CMANE SELECT
  • NC_000017.10:g.3563529G>C
Links:
dbSNP: rs2142982540
NCBI 1000 Genomes Browser:
rs2142982540
Molecular consequence:
  • NM_001031681.3:c.971-1G>C - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001374492.1:c.971-1G>C - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001374493.1:c.530-1G>C - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001374494.1:c.530-1G>C - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001374495.1:c.530-1G>C - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001374496.1:c.530-1G>C - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_004937.3:c.971-1G>C - splice acceptor variant - [Sequence Ontology: SO:0001574]
Observations:
4

Condition(s)

Name:
Nephropathic cystinosis (CTNS)
Synonyms:
Lysosomal cystine transport protein, defect of; Cystinosin, 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
SCV001554457Congenital and Hereditary Diseases, Charles Nicolle Hospital
no assertion criteria provided
Likely pathogenic
(Mar 1, 2021) 		germlineclinical testing

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
North Africangermlineyes134not providednot providednot providedclinical testing

Details of each submission

From Congenital and Hereditary Diseases, Charles Nicolle Hospital, SCV001554457.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1North African13not providednot providedclinical testingnot provided

Description

DNA sequencing revealed novel homozygous splicing mutation NM_001031681: c.971-1G>C in 6 patients belonging to 4 families. All parents of these patients were consanguineous and were confirmed to be heterozygous carriers. The splicing NM_001031681: c.971-1G>C segregated according to a recessive model with full penetrance. NM_001031681: c.971-1G>C was not referenced in the NHLBI Exome Variant Server or in the ClinVar database. Analysis of NM_001031681: c.971-1G>C with Alamut, predicted change at acceptor site of intron 11, 1 bp downstream and the activation of a cryptic acceptor site at +5 bp. The predicted protein will be p.D324VfsX31.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot provided13not provided4not provided

Last Updated: Dec 24, 2023