NM_153766.3(KCNJ1):c.514A>C (p.Thr172Pro) AND Bartter disease type 2

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Oct 27, 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:: RCV003388812.1

Allele description [Variation Report for NM_153766.3(KCNJ1):c.514A>C (p.Thr172Pro)]

NM_153766.3(KCNJ1):c.514A>C (p.Thr172Pro)

Gene:

KCNJ1:potassium inwardly rectifying channel subfamily J member 1 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

11q24.3

Genomic location:

Preferred name:

NM_153766.3(KCNJ1):c.514A>C (p.Thr172Pro)

HGVS:

NC_000011.10:g.128839730T>G
NG_009379.1:g.32644A>C
NM_000220.6:c.571A>C
NM_153764.3:c.514A>C
NM_153765.3:c.565A>C
NM_153766.3:c.514A>CMANE SELECT
NM_153767.4:c.514A>C
NP_000211.1:p.Thr191Pro
NP_722448.1:p.Thr172Pro
NP_722449.3:p.Thr189Pro
NP_722450.1:p.Thr172Pro
NP_722451.1:p.Thr172Pro
NC_000011.9:g.128709625T>G

Protein change:

T172P

Molecular consequence:

NM_000220.6:c.571A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_153764.3:c.514A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_153765.3:c.565A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_153766.3:c.514A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_153767.4:c.514A>C - missense variant - [Sequence Ontology: SO:0001583]

Observations:

Condition(s)

Name:: Bartter disease type 2
Synonyms:: HYPOKALEMIC ALKALOSIS WITH HYPERCALCIURIA 2, ANTENATAL; Hyperprostaglandin E syndrome 2; Bartter syndrome, type 2, antenatal
Identifiers:: MONDO: MONDO:0009424; MedGen: C1855849; Orphanet: 112; OMIM: 241200

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004098992	Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Oct 27, 2023)	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

SCV004098992

Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(Oct 27, 2023)

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	yes	1	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

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 Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital, SCV004098992.1

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

Description

This heterozygous mis-sense variant is identified in a 5 year malewith polyurea, hypokalemia, GDD, dandy walker malformation, nephrocalcinosis and optic disc hypoplasia. This nucleotide change is absent in gnomAD database [PM2]. Insilico prediction [REVEL=0.81] predicts deleterious nature of this variant [PP3]. This variant is identified in trans [PM3] with another previously pathogenic reported variant p.Leu220Phe (Clinvar Variation ID: 872043). To our knowledge, clinvar entry for Thr191Pro variant is not available. Based on the clinical correlation and available evidence, this variant is classified as "Pathogenic".

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

Last Updated: Nov 4, 2023

ClinVar

Relating variation to medicine