NM_004937.3(CTNS):c.40del (p.Pro13_Leu14insTer) AND Nephropathic cystinosis

Germline classification:: Pathogenic/Likely pathogenic (2 submissions)
Last evaluated:: Jan 11, 2024
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:: RCV000672996.11

Allele description [Variation Report for NM_004937.3(CTNS):c.40del (p.Pro13_Leu14insTer)]

NM_004937.3(CTNS):c.40del (p.Pro13_Leu14insTer)

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.40del (p.Pro13_Leu14insTer)

HGVS:

NC_000017.11:g.3640246del
NG_012489.2:g.8779del
NG_052852.1:g.1080del
NM_001031681.3:c.40del
NM_001374492.1:c.40del
NM_001374493.1:c.-317del
NM_001374494.1:c.-381+2930del
NM_001374495.1:c.-238del
NM_001374496.1:c.-296+2930del
NM_004937.3:c.40delMANE SELECT
NP_001026851.2:p.Pro13_Leu14insTer
NP_001361421.1:p.Pro13_Leu14insTer
NP_004928.2:p.Pro13_Leu14insTer
NC_000017.10:g.3543537del
NC_000017.10:g.3543540del
NM_004937.2:c.40delC

Links:

dbSNP: rs1555558099

NCBI 1000 Genomes Browser:

rs1555558099

Molecular consequence:

NM_001374493.1:c.-317del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001374495.1:c.-238del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001374494.1:c.-381+2930del - intron variant - [Sequence Ontology: SO:0001627]
NM_001374496.1:c.-296+2930del - intron variant - [Sequence Ontology: SO:0001627]
NM_001031681.3:c.40del - nonsense - [Sequence Ontology: SO:0001587]
NM_001374492.1:c.40del - nonsense - [Sequence Ontology: SO:0001587]
NM_004937.3:c.40del - nonsense - [Sequence Ontology: SO:0001587]

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
SCV000798158	Counsyl	criteria provided, single submitter (Counsyl Autosomal Recessive and X-Linked Classification Criteria (2018))	Likely pathogenic (Feb 27, 2018)	unknown	clinical testing	PubMed (1) [See all records that cite this PMID] Citation Link,
SCV004212977	Baylor Genetics	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Jan 11, 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

SCV000798158

Counsyl

criteria provided, single submitter

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

Likely pathogenic
(Feb 27, 2018)

unknown

clinical testing

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

Citation Link,

SCV004212977

Baylor Genetics

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(Jan 11, 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

Analysis of the CTNS gene in nephropathic cystinosis Mexican patients: report of four novel mutations and identification of a false positive 57-kb deletion genotype with LDM-2/exon 4 multiplex PCR assay.

Alcántara-Ortigoza MA, Belmont-Martínez L, Vela-Amieva M, González-Del Angel A.

Genet Test. 2008 Sep;12(3):409-14. doi: 10.1089/gte.2008.0014.

PubMed [citation]

PMID:: 18752449

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, SCV000798158.1

#	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, SCV004212977.2

#	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

Last Updated: Jan 13, 2025

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