NM_004937.3(CTNS):c.300T>A (p.Tyr100Ter) AND multiple conditions

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Jan 20, 2023
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:: RCV003770373.2

Allele description [Variation Report for NM_004937.3(CTNS):c.300T>A (p.Tyr100Ter)]

NM_004937.3(CTNS):c.300T>A (p.Tyr100Ter)

Genes:

CTNS-AS1:CTNS antisense RNA 1 [Gene - HGNC]
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.300T>A (p.Tyr100Ter)

HGVS:

NC_000017.11:g.3655072T>A
NG_012489.2:g.23605T>A
NM_001031681.3:c.300T>A
NM_001374492.1:c.300T>A
NM_001374493.1:c.-142T>A
NM_001374494.1:c.-142T>A
NM_001374495.1:c.-142T>A
NM_001374496.1:c.-142T>A
NM_004937.3:c.300T>AMANE SELECT
NP_001026851.2:p.Tyr100Ter
NP_001361421.1:p.Tyr100Ter
NP_004928.2:p.Tyr100Ter
NC_000017.10:g.3558366T>A
NG_012489.1:g.23605T>A

Protein change:

Y100*

Links:

dbSNP: rs376042415

NCBI 1000 Genomes Browser:

rs376042415

Molecular consequence:

NM_001374493.1:c.-142T>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001374494.1:c.-142T>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001374495.1:c.-142T>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001374496.1:c.-142T>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001031681.3:c.300T>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001374492.1:c.300T>A - nonsense - [Sequence Ontology: SO:0001587]
NM_004937.3:c.300T>A - nonsense - [Sequence Ontology: SO:0001587]

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

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004590784	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Jan 20, 2023)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 9537412, 27102039, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004590784

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Jan 20, 2023)

germline

clinical testing

PubMed (3)
[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 novel gene encoding an integral membrane protein is mutated in nephropathic cystinosis.

Town M, Jean G, Cherqui S, Attard M, Forestier L, Whitmore SA, Callen DF, Gribouval O, Broyer M, Bates GP, van't Hoff W, Antignac C.

Nat Genet. 1998 Apr;18(4):319-24.

PubMed [citation]

PMID:: 9537412

Cystinosis: a review.

Elmonem MA, Veys KR, Soliman NA, van Dyck M, van den Heuvel LP, Levtchenko E.

Orphanet J Rare Dis. 2016 Apr 22;11:47. doi: 10.1186/s13023-016-0426-y. Review.

PubMed [citation]

PMID:: 27102039
PMCID:: PMC4841061

See all PubMed Citations (3)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV004590784.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (3)

Description

For these reasons, this variant has been classified as Pathogenic. ClinVar contains an entry for this variant (Variation ID: 984078). 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.Tyr100*) in the CTNS gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in CTNS are known to be pathogenic (PMID: 9537412, 27102039).

#	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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