NC_000003.11:g.(?_190120106)_(190127825_?)del AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Oct 24, 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:: RCV003109540.5

Allele description [Variation Report for NC_000003.11:g.(?_190120106)_(190127825_?)del]

NC_000003.11:g.(?_190120106)_(190127825_?)del

Gene:: CLDN16:claudin 16 [Gene - OMIM - HGNC]
Variant type:: Deletion
Cytogenetic location:: 3q28
Genomic location:: Chr3: 190120106 - 190127825 (on Assembly GRCh37)
Preferred name:: NC_000003.11:g.(?_190120106)_(190127825_?)del
HGVS:: NC_000003.11:g.(?_190120106)_(190127825_?)del
This HGVS expression did not pass validation

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003791520	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Oct 24, 2023)	germline	clinical testing	PubMed (7) [See all records that cite these PMIDs] 26136118, 32710267, 10878661, 11518780, 18003771, 25477417, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003791520

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Oct 24, 2023)

germline

clinical testing

PubMed (7)
[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

Identification of the first large deletion in the CLDN16 gene in a patient with FHHNC and late-onset of chronic kidney disease: case report.

Yamaguti PM, dos Santos PA, Leal BS, Santana VB, Mazzeu JF, Acevedo AC, Neves Fde A.

BMC Nephrol. 2015 Jul 2;16:92. doi: 10.1186/s12882-015-0079-4.

PubMed [citation]

PMID:: 26136118
PMCID:: PMC4487846

Hypomagnesemia with Hypercalciuria Leading to Nephrocalcinosis, Amelogenesis Imperfecta, and Short Stature in a Child Carrying a Homozygous Deletion in the CLDN16 Gene.

Radonsky V, Kizys MML, Dotto RP, Esper PLG, Heilberg IP, Dias-da-Silva MR, Lazaretti-Castro M.

Calcif Tissue Int. 2020 Oct;107(4):403-408. doi: 10.1007/s00223-020-00726-y. Epub 2020 Jul 24.

PubMed [citation]

PMID:: 32710267

See all PubMed Citations (7)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV003791520.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (7)

Description

This variant is a gross deletion of the genomic region encompassing exon(s) 2-5 of the CLDN16 gene, which includes the termination codon. This deletion extends beyond the assayed region for this gene and therefore may encompass additional genes. While this deletion is not anticipated to lead to nonsense mediated decay, it is expected to alter mRNA translation or result in a truncated protein product. A similar copy number variant has been observed in individuals with CLDN16-related conditions (PMID: 26136118, 32710267). This variant disrupts a region of the CLDN16 protein in which other variant(s) (p.Gly239Arg) have been determined to be pathogenic (PMID: 10878661, 11518780, 18003771, 25477417). This suggests that this is a clinically significant region of the protein, and that variants that disrupt it are likely to be disease-causing. 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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