NC_000017.11:g.3660238_3660245del AND multiple conditions

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Jul 17, 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:: RCV002857093.3

Allele description [Variation Report for NC_000017.11:g.3660238_3660245del]

NC_000017.11:g.3660238_3660245del

Gene:

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

Variant type:

Deletion

Cytogenetic location:

17p13.2

Genomic location:

Preferred name:

NC_000017.11:g.3660238_3660245del

HGVS:

NC_000017.11:g.3660238_3660245del
NG_012489.2:g.28771_28778del
NC_000017.10:g.3563529_3563536del
NC_000017.10:g.3563532_3563539del

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

Recent activity

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endosomal integral membrane protein, putative [Trypanosoma brucei gambiense DAL9...
endosomal integral membrane protein, putative [Trypanosoma brucei gambiense DAL972]
gi|261327143|emb|CBH10119.1|

Protein
Mus musculus ORM1-like 2 (S. cerevisiae), mRNA (cDNA clone MGC:7263 IMAGE:348483...
Mus musculus ORM1-like 2 (S. cerevisiae), mRNA (cDNA clone MGC:7263 IMAGE:3484833), complete cds
gi|12805352|gb|BC002146.1|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003222032	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Jul 17, 2022)	germline	clinical testing	PubMed (6) [See all records that cite these PMIDs] 11565547, 12204010, 12825071, 21786142, 23640116, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003222032

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Jul 17, 2022)

germline

clinical testing

PubMed (6)
[See all records that cite these PMIDs]

Help

Summary from all submissions

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

Citations

PubMed

A G339R mutation in the CTNS gene is a common cause of nephropathic cystinosis in the south western Ontario Amish Mennonite population.

Rupar CA, Matsell D, Surry S, Siu V.

J Med Genet. 2001 Sep;38(9):615-6. No abstract available.

PubMed [citation]

PMID:: 11565547
PMCID:: PMC1734937

Analysis of the CTNS gene in patients of German and Swiss origin with nephropathic cystinosis.

Kiehntopf M, Schickel J, Gönne Bv, Koch HG, Superti-Furga A, Steinmann B, Deufel T, Harms E.

Hum Mutat. 2002 Sep;20(3):237.

PubMed [citation]

PMID:: 12204010

See all PubMed Citations (6)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV003222032.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (6)

Description

This variant has not been reported in the literature in individuals affected with CTNS-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change creates a premature translational stop signal (p.Gln325Alafs*37) in the CTNS gene. While this is not anticipated to result in nonsense mediated decay, it is expected to disrupt the last 43 amino acid(s) of the CTNS protein. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. For these reasons, this variant has been classified as Pathogenic. This variant disrupts a region of the CTNS protein in which other variant(s) (p.Gly339Arg) have been determined to be pathogenic (PMID: 11565547, 12204010, 12825071, 21786142, 23640116). This suggests that this is a clinically significant region of the protein, and that variants that disrupt it are likely to be disease-causing.

#	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: Sep 29, 2024

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