NM_004937.3(CTNS):c.771_793del (p.Gly258fs) AND Cystinosis

Germline classification:: Pathogenic (3 submissions)
Last evaluated:: Jul 5, 2017
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV000586519.12

Allele description [Variation Report for NM_004937.3(CTNS):c.771_793del (p.Gly258fs)]

NM_004937.3(CTNS):c.771_793del (p.Gly258fs)

Gene:

CTNS:cystinosin, lysosomal cystine transporter [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

17p13.2

Genomic location:

Preferred name:

NM_004937.3(CTNS):c.771_793del (p.Gly258fs)

HGVS:

NC_000017.11:g.3658094_3658116del
NG_012489.2:g.26627_26649del
NM_001031681.3:c.771_793del
NM_001374492.1:c.771_793del
NM_001374493.1:c.330_352del
NM_001374494.1:c.330_352del
NM_001374495.1:c.330_352del
NM_001374496.1:c.330_352del
NM_004937.3:c.771_793delMANE SELECT
NP_001026851.2:p.Gly258fs
NP_001026851.2:p.Gly258fs
NP_001361421.1:p.Gly258fs
NP_001361422.1:p.Gly111fs
NP_001361423.1:p.Gly111fs
NP_001361424.1:p.Gly111fs
NP_001361425.1:p.Gly111fs
NP_004928.2:p.Gly258fs
NC_000017.10:g.3561376_3561398del
NC_000017.10:g.3561388_3561410del
NM_001031681.2:c.771_793del
NM_004937.2:c.771_793del23

Protein change:

G111fs

Links:

dbSNP: rs759623796

NCBI 1000 Genomes Browser:

rs759623796

Molecular consequence:

NM_001031681.3:c.771_793del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001374492.1:c.771_793del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001374493.1:c.330_352del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001374494.1:c.330_352del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001374495.1:c.330_352del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001374496.1:c.330_352del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_004937.3:c.771_793del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Name:: Cystinosis
Synonyms:: Cystine diathesis; Cystine disease; Cystine storage disease; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0016239; MedGen: C4316899

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000698526	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	criteria provided, single submitter (LabCorp Variant Classification Summary - May 2015)	Pathogenic (Jul 5, 2017)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 26266097, 10556299 LabCorp Variant Classification Summary - May 2015.docx, Citation Link,
SCV001424396	Centogene AG - the Rare Disease Company	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV002093236	Natera, Inc.	no assertion criteria provided	Pathogenic (Jan 26, 2021)	germline	clinical testing

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000698526

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)

Pathogenic
(Jul 5, 2017)

germline

clinical testing

PubMed (2)
[See all records that cite these PMIDs]

LabCorp Variant Classification Summary - May 2015.docx,

Citation Link,

SCV001424396

Centogene AG - the Rare Disease Company

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic

germline

clinical testing

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

SCV002093236

Natera, Inc.

no assertion criteria provided

Pathogenic
(Jan 26, 2021)

germline

clinical testing

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Genetic basis of cystinosis in Tunisian patients: Identification of novel mutation in CTNS gene.

Chkioua L, Khedhiri S, Grissa O, Aloui C, Turkia HB, Ferchichi S, Miled A, Froissart R, Acquaviva C, Laradi S.

Meta Gene. 2015 Sep;5:144-9. doi: 10.1016/j.mgene.2015.07.003.

PubMed [citation]

PMID:: 26266097
PMCID:: PMC4528043

Severity of phenotype in cystinosis varies with mutations in the CTNS gene: predicted effect on the model of cystinosin.

Attard M, Jean G, Forestier L, Cherqui S, van't Hoff W, Broyer M, Antignac C, Town M.

Hum Mol Genet. 1999 Dec;8(13):2507-14.

PubMed [citation]

PMID:: 10556299

See all PubMed Citations (3)

Details of each submission

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV000698526.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (2)

Description

Variant summary: The variant results in the deletion of a 23 nucleotides leading to a termination codon at position 288 of CTNS. The variant was present at a low frequency in the large and broad cohorts of the ExAC project (3/121,076 chromosomes) while it was observed in multiple CTNS patients in the literature. Considering all evidence, the variant was classified as pathogenic.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Centogene AG - the Rare Disease Company, SCV001424396.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Natera, Inc., SCV002093236.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Oct 26, 2024

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