NM_006580.4(CLDN16):c.383G>A (p.Gly128Asp) AND Primary hypomagnesemia

Germline classification:: Likely pathogenic (2 submissions)
Last evaluated:: Nov 21, 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:: RCV000006291.4

Allele description [Variation Report for NM_006580.4(CLDN16):c.383G>A (p.Gly128Asp)]

NM_006580.4(CLDN16):c.383G>A (p.Gly128Asp)

Gene:

CLDN16:claudin 16 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

3q28

Genomic location:

Preferred name:

NM_006580.4(CLDN16):c.383G>A (p.Gly128Asp)

Other names:

G198D

HGVS:

NC_000003.12:g.190408314G>A
NG_008149.1:g.25263G>A
NM_001378492.1:c.383G>A
NM_001378493.1:c.383G>A
NM_006580.4:c.383G>AMANE SELECT
NP_001365421.1:p.Gly128Asp
NP_001365422.1:p.Gly128Asp
NP_006571.2:p.Gly128Asp
NC_000003.11:g.190126103G>A
Q9Y5I7:p.Gly198Asp

Protein change:

G128D; GLY198ASP

Links:

UniProtKB: Q9Y5I7#VAR_008176; OMIM: 603959.0004; dbSNP: rs104893723

NCBI 1000 Genomes Browser:

rs104893723

Molecular consequence:

NM_001378492.1:c.383G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001378493.1:c.383G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_006580.4:c.383G>A - 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

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000026473	OMIM	no assertion criteria provided	Pathogenic (Jul 2, 1999)	germline	literature only	PubMed (1) [See all records that cite this PMID]
SCV002782914	Fulgent Genetics, Fulgent Genetics	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (Nov 21, 2021)	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

SCV000026473

OMIM

no assertion criteria provided

Pathogenic
(Jul 2, 1999)

germline

literature only

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

SCV002782914

Fulgent Genetics, Fulgent Genetics

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic
(Nov 21, 2021)

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

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, SCV000026473.2

#	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 G-to-A transition in the first base of exon 4, which caused a gly-to-asp substitution at codon 198 of the PCLN1 gene in 2 families with primary hypomagnesemia (HOMG3; 248250). This mutation was found in homozygosity in 1 kindred and in compound heterozygosity in another kindred (K106). The second mutation in kindred K106 was ser235 to phe (603959.0009).

#	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 Fulgent Genetics, Fulgent Genetics, SCV002782914.1

#	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

Last Updated: Jan 7, 2023

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