NC_000017.11:g.(?_3636418)_(3658185_?)del AND multiple conditions

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Dec 31, 2019
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:: RCV000807914.3

Allele description [Variation Report for NC_000017.11:g.(?_3636418)_(3658185_?)del]

NC_000017.11:g.(?_3636418)_(3658185_?)del

Genes:

LOC130059980:ATAC-STARR-seq lymphoblastoid active region 11511 [Gene]
LOC130059981:ATAC-STARR-seq lymphoblastoid silent region 8015 [Gene]
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:

NC_000017.11:g.(?_3636418)_(3658185_?)del

HGVS:

NC_000017.11:g.(?_3636418)_(3658185_?)del
NC_000017.10:g.(?_3539712)_(3561479_?)del

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:: 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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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000947994	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Dec 31, 2019)	germline	clinical testing	PubMed (8) [See all records that cite these PMIDs] 10625078, 28405942, 12204010, 21546516, 18186520, 9792862, 27734949, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000947994

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Dec 31, 2019)

germline

clinical testing

PubMed (8)
[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

Ocular nonnephropathic cystinosis: clinical, biochemical, and molecular correlations.

Anikster Y, Lucero C, Guo J, Huizing M, Shotelersuk V, Bernardini I, McDowell G, Iwata F, Kaiser-Kupfer MI, Jaffe R, Thoene J, Schneider JA, Gahl WA.

Pediatr Res. 2000 Jan;47(1):17-23.

PubMed [citation]

PMID:: 10625078

First Successful Conception Induced by a Male Cystinosis Patient.

Veys KR, D'Hauwers KW, van Dongen AJCM, Janssen MC, Besouw MTP, Goossens E, van den Heuvel LP, Wetzels AAMM, Levtchenko EN.

JIMD Rep. 2018;38:1-6. doi: 10.1007/8904_2017_19. Epub 2017 Apr 13.

PubMed [citation]

PMID:: 28405942
PMCID:: PMC5874217

See all PubMed Citations (8)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV000947994.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (8)

Description

This variant is a gross deletion of the genomic region encompassing exons 1-10 of the CTNS gene, which includes the initiator codon. The 5' end of this event is unknown as it extends beyond the assayed region for this gene and therefore may encompass additional genes. The 3' boundary is likely confined to intron 10 of the CTNS gene. This is expected to result in an absent or disrupted protein product. A 57 kb deletion of exons 1-10 and including other genes has been reported to be common in individuals affected with cystinosis (PMID: 10625078, 21546516, 12204010, 28405942, 27734949, 9792862, 18186520). Loss-of-function variants in CTNS are known to be pathogenic (PMID: 9537412, 27102039). For these reasons, this variant has been 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

Last Updated: Sep 29, 2024

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