NM_001282534.2(KCNK9):c.710C>A (p.Ala237Asp) AND Birk-Barel syndrome

Germline classification:: Likely pathogenic (2 submissions)
Last evaluated:: Jan 1, 2019
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:: RCV001262218.4

Allele description [Variation Report for NM_001282534.2(KCNK9):c.710C>A (p.Ala237Asp)]

NM_001282534.2(KCNK9):c.710C>A (p.Ala237Asp)

Gene:

KCNK9:potassium two pore domain channel subfamily K member 9 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

8q24.3

Genomic location:

Preferred name:

NM_001282534.2(KCNK9):c.710C>A (p.Ala237Asp)

HGVS:

NC_000008.11:g.139618673G>T
NG_012842.3:g.89384C>A
NM_001282534.2:c.710C>AMANE SELECT
NP_001269463.1:p.Ala237Asp
LRG_1042t1:c.710C>A
LRG_1042:g.89384C>A
LRG_1042p1:p.Ala237Asp
NC_000008.10:g.140630916G>T
NG_012842.2:g.89384C>A
NM_001282534.1:c.710C>A
NR_104210.2:n.841C>A

Protein change:

A237D; ALA237ASP

Links:

OMIM: 605874.0002; dbSNP: rs1814677892

NCBI 1000 Genomes Browser:

rs1814677892

Molecular consequence:

NM_001282534.2:c.710C>A - missense variant - [Sequence Ontology: SO:0001583]
NR_104210.2:n.841C>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:: Birk-Barel syndrome
Synonyms:: Birk Barel mental retardation dysmorphism syndrome; Mental retardation with hypotonia and facial dysmorphism
Identifiers:: MONDO: MONDO:0012856; MedGen: C2676770; Orphanet: 166108; OMIM: 612292

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001440010	Institute of Human Genetics, University of Leipzig Medical Center	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (Jan 1, 2019)	de novo	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV001448182	OMIM	no assertion criteria provided	Pathogenic (Nov 30, 2020)	germline	literature only	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001440010

Institute of Human Genetics, University of Leipzig Medical Center

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic
(Jan 1, 2019)

de novo

clinical testing

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

SCV001448182

OMIM

no assertion criteria provided

Pathogenic
(Nov 30, 2020)

germline

literature only

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	de novo	yes	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

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

Novel variant in the KCNK9 gene in a girl with Birk Barel syndrome.

Šedivá M, Laššuthová P, Zámečník J, Sedláčková L, Seeman P, Haberlová J.

Eur J Med Genet. 2020 Jan;63(1):103619. doi: 10.1016/j.ejmg.2019.01.009. Epub 2019 Jan 25.

PubMed [citation]

PMID:: 30690205

Details of each submission

From Institute of Human Genetics, University of Leipzig Medical Center, SCV001440010.1

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

Description

This variant was identified as de novo.

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

From OMIM, SCV001448182.2

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

Description

By whole-exome sequencing in a 17-year-old girl with Birk-Barel syndrome (BIBARS; 612292), Sediva et al. (2020) identified a heterozygous c.710C-A transversion (c.710C-A, NM_001282534.1) in exon 2 of the KCNK9 gene, resulting in an ala237-to-asp (A237D) substitution at a highly conserved residue. The patient's father and maternal grandparents did not have the mutation; her mother was not available for testing. Functional studies were not performed. The patient had axonal motor neuropathy, cleft palate, developmental delay, and hypotonia.

#	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

Last Updated: Aug 5, 2023

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