NM_153766.3(KCNJ1):c.302C>T (p.Pro101Leu) AND Bartter disease type 2

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Oct 19, 2020
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:: RCV002470431.1

Allele description [Variation Report for NM_153766.3(KCNJ1):c.302C>T (p.Pro101Leu)]

NM_153766.3(KCNJ1):c.302C>T (p.Pro101Leu)

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.302C>T (p.Pro101Leu)

HGVS:

NC_000011.10:g.128839942G>A
NG_009379.1:g.32432C>T
NM_000220.6:c.359C>T
NM_153764.3:c.302C>T
NM_153765.3:c.353C>T
NM_153766.3:c.302C>TMANE SELECT
NM_153767.4:c.302C>T
NP_000211.1:p.Pro120Leu
NP_722448.1:p.Pro101Leu
NP_722449.3:p.Pro118Leu
NP_722450.1:p.Pro101Leu
NP_722451.1:p.Pro101Leu
NC_000011.9:g.128709837G>A
NM_000220.4:c.359C>T

Protein change:

P101L

Molecular consequence:

NM_000220.6:c.359C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_153764.3:c.302C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_153765.3:c.353C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_153766.3:c.302C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_153767.4:c.302C>T - missense variant - [Sequence Ontology: SO:0001583]

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
SCV002767868	Victorian Clinical Genetics Services, Murdoch Childrens Research Institute See additional submitters Shariant Australia, Australian Genomics	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (Oct 19, 2020)	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

SCV002767868

Victorian Clinical Genetics Services, Murdoch Childrens Research Institute

See additional submitters

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance
(Oct 19, 2020)

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

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 Victorian Clinical Genetics Services, Murdoch Childrens Research Institute, SCV002767868.1

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

Description

Based on the classification scheme VCGS_Germline_v1.3.3, this variant is classified as 3B-VUS. Following criteria are met: 0102 - Loss of function is a known mechanism of disease in this gene and is associated with Bartter syndrome, type 2 (MIM#241200). (I) 0106 - This gene is associated with autosomal recessive disease. (I) 0200 - Variant is predicted to result in a missense amino acid change from proline to leucine. (I) 0251 - This variant is heterozygous. (I) 0301 - Variant is absent from gnomAD (both v2 and v3). (SP) 0501 - Missense variant consistently predicted to be damaging by multiple in silico tools or highly conserved with a major amino acid change. (SP) 0600 - Variant is located in the annotated inward rectifier potassium channel domain (NCBI, PDB). (I) 0705 - No comparable missense variants have previous evidence for pathogenicity. (I) 0807 - This variant has no previous evidence of pathogenicity. (I) 0905 - No published segregation evidence has been identified for this variant. (I) 1007 - No published functional evidence has been identified for this variant. (I) 1206 - This variant has been shown to be paternally inherited at an external laboratory (Fulgent Genetics). (I) Legend: (SP) - Supporting pathogenic, (I) - Information, (SB) - Supporting benign

#	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: Jan 21, 2023

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