NM_004937.3(CTNS):c.225+5_225+8del AND Nephropathic cystinosis

Germline classification:: Likely pathogenic (2 submissions)
Last evaluated:: Mar 18, 2024
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:: RCV000665684.5

Allele description [Variation Report for NM_004937.3(CTNS):c.225+5_225+8del]

NM_004937.3(CTNS):c.225+5_225+8del

Gene:

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

Variant type:

Microsatellite

Cytogenetic location:

17p13.2

Genomic location:

Preferred name:

NM_004937.3(CTNS):c.225+5_225+8del

HGVS:

NC_000017.11:g.3648932GTAA[1]
NG_012489.2:g.17465GTAA[1]
NM_001031681.3:c.225+5_225+8del
NM_001374492.1:c.225+5_225+8del
NM_001374493.1:c.-217+1414_-217+1417del
NM_001374494.1:c.-217+5_-217+8del
NM_001374495.1:c.-216-6062_-216-6059del
NM_001374496.1:c.-217+1414_-217+1417del
NM_004937.3:c.225+5_225+8delMANE SELECT
NC_000017.10:g.3552224_3552227del
NC_000017.10:g.3552226GTAA[1]
NM_004937.2:c.225+5_225+8delGTAA

Links:

dbSNP: rs1555561048

NCBI 1000 Genomes Browser:

rs1555561048

Molecular consequence:

NM_001374493.1:c.-217+1414_-217+1417del - intron variant - [Sequence Ontology: SO:0001627]
NM_001374495.1:c.-216-6062_-216-6059del - intron variant - [Sequence Ontology: SO:0001627]
NM_001374496.1:c.-217+1414_-217+1417del - intron variant - [Sequence Ontology: SO:0001627]
NM_001031681.3:c.225+5_225+8del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001374492.1:c.225+5_225+8del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001374494.1:c.-217+5_-217+8del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_004937.3:c.225+5_225+8del - splice donor variant - [Sequence Ontology: SO:0001575]

Condition(s)

Name:: Nephropathic cystinosis (CTNS)
Synonyms:: CYSTINOSIN, DEFECT OF; LYSOSOMAL CYSTINE TRANSPORT PROTEIN, 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
SCV004212939	Baylor Genetics	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (Mar 18, 2024)	unknown	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004212939

Baylor Genetics

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic
(Mar 18, 2024)

unknown

clinical testing

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

Help

Summary from all submissions

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

Citations

PubMed

Identification of 14 novel CTNS mutations and characterization of seven splice site mutations associated with cystinosis.

Kalatzis V, Cohen-Solal L, Cordier B, Frishberg Y, Kemper M, Nuutinen EM, Legrand E, Cochat P, Antignac C.

Hum Mutat. 2002 Dec;20(6):439-46.

PubMed [citation]

PMID:: 12442267

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee.

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From Counsyl, SCV000789843.1

#	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	unknown	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Baylor Genetics, SCV004212939.2

#	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	unknown	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Flagged submissions

Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000789843	Counsyl	flagged submission Reason: Claim with insufficient supporting evidence Notes: None (Counsyl Autosomal Recessive and X-Linked Classification Criteria (2018))	Uncertain significance (Feb 24, 2017)	unknown	clinical testing	PubMed (1) [See all records that cite this PMID] Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000789843

Counsyl

flagged submission

Reason: Claim with insufficient supporting evidence

Notes: None

(Counsyl Autosomal Recessive and X-Linked Classification Criteria (2018))

Uncertain significance
(Feb 24, 2017)

unknown

clinical testing

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

Citation Link

Last Updated: Jan 13, 2025

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