NM_006580.4(CLDN16):c.485T>G (p.Phe162Cys) AND Primary hypomagnesemia

Germline classification:: Uncertain significance (2 submissions)
Last evaluated:: Mar 26, 2021
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:: RCV000006294.7

Allele description [Variation Report for NM_006580.4(CLDN16):c.485T>G (p.Phe162Cys)]

NM_006580.4(CLDN16):c.485T>G (p.Phe162Cys)

Gene:

CLDN16:claudin 16 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

3q28

Genomic location:

Preferred name:

NM_006580.4(CLDN16):c.485T>G (p.Phe162Cys)

HGVS:

NC_000003.12:g.190408416T>G
NG_008149.1:g.25365T>G
NM_001378492.1:c.485T>G
NM_001378493.1:c.485T>G
NM_006580.4:c.485T>GMANE SELECT
NP_001365421.1:p.Phe162Cys
NP_001365422.1:p.Phe162Cys
NP_006571.1:p.Phe232Cys
NP_006571.2:p.Phe162Cys
NC_000003.11:g.190126205T>G
NM_006580.3:c.695T>G
Q9Y5I7:p.Phe232Cys

Protein change:

F162C; PHE232CYS

Links:

UniProtKB: Q9Y5I7#VAR_008177; OMIM: 603959.0007; dbSNP: rs104893726

NCBI 1000 Genomes Browser:

rs104893726

Molecular consequence:

NM_001378492.1:c.485T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001378493.1:c.485T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_006580.4:c.485T>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Primary hypomagnesemia (HOMG3)
Synonyms:: HYPOMAGNESEMIA 3, RENAL; HYPOMAGNESEMIA, PRIMARY, DUE TO DEFECT IN RENAL TUBULAR TRANSPORT OF MAGNESIUM; Magnesium, defect in renal tubular transport of; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0009550; MedGen: C0268448; Orphanet: 31043; OMIM: 248250

Recent activity

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phosphoinositide 3-kinase adapter protein 1 [Homo sapiens]
phosphoinositide 3-kinase adapter protein 1 [Homo sapiens]
gi|45505139|ref|NP_689522.2|

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000026476	OMIM	no assertion criteria provided	Pathogenic (Jul 2, 1999)	germline	literature only	PubMed (1) [See all records that cite this PMID]
SCV003832395	Revvity Omics, Revvity	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (Mar 26, 2021)	germline	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

SCV000026476

OMIM

no assertion criteria provided

Pathogenic
(Jul 2, 1999)

germline

literature only

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

SCV003832395

Revvity Omics, Revvity

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance
(Mar 26, 2021)

germline

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	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	not provided	not provided	not provided	not provided	not provided	not provided	literature only

Citations

PubMed

Paracellin-1, a renal tight junction protein required for paracellular Mg2+ resorption.

Simon DB, Lu Y, Choate KA, Velazquez H, Al-Sabban E, Praga M, Casari G, Bettinelli A, Colussi G, Rodriguez-Soriano J, McCredie D, Milford D, Sanjad S, Lifton RP.

Science. 1999 Jul 2;285(5424):103-6.

PubMed [citation]

PMID:: 10390358

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 OMIM, SCV000026476.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	literature only	PubMed (1)

Description

Using SSCP and sequencing, Simon et al. (1999) identified a a phe232-to-cys substitution in the PCLN1 gene in patients with primary hypomagnesemia (HOMG3; 248250).

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	not provided	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Revvity Omics, Revvity, SCV003832395.2

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

Last Updated: Mar 16, 2024

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