NM_001291415.2(KDM6A):c.3991C>T (p.Arg1331Ter) AND Kabuki syndrome 2

Germline classification:: Pathogenic/Likely pathogenic (3 submissions)
Last evaluated:: Dec 22, 2018
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV000197668.4

Allele description [Variation Report for NM_001291415.2(KDM6A):c.3991C>T (p.Arg1331Ter)]

NM_001291415.2(KDM6A):c.3991C>T (p.Arg1331Ter)

Gene:

KDM6A:lysine demethylase 6A [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

Xp11.3

Genomic location:

Preferred name:

NM_001291415.2(KDM6A):c.3991C>T (p.Arg1331Ter)

HGVS:

NC_000023.11:g.45090821C>T
NG_016260.1:g.222644C>T
NM_001291415.2:c.3991C>TMANE SELECT
NM_001291416.2:c.3856C>T
NM_001291417.2:c.3700C>T
NM_001291418.2:c.3598C>T
NM_001291421.2:c.2947C>T
NM_021140.4:c.3835C>T
NP_001278344.1:p.Arg1331Ter
NP_001278345.1:p.Arg1286Ter
NP_001278346.1:p.Arg1234Ter
NP_001278347.1:p.Arg1200Ter
NP_001278350.1:p.Arg983Ter
NP_066963.2:p.Arg1279Ter
NP_066963.2:p.Arg1279Ter
LRG_616t1:c.3991C>T
LRG_616:g.222644C>T
NC_000023.10:g.44950066C>T
NM_001291415.1:c.3991C>T
NM_021140.2:c.3835C>T
NM_021140.3:c.3835C>T
NR_111960.2:n.4118C>T

Protein change:

R1200*

Links:

dbSNP: rs863224886

NCBI 1000 Genomes Browser:

rs863224886

Molecular consequence:

NR_111960.2:n.4118C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NM_001291415.2:c.3991C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001291416.2:c.3856C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001291417.2:c.3700C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001291418.2:c.3598C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001291421.2:c.2947C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_021140.4:c.3835C>T - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Name:: Kabuki syndrome 2 (KABUK2)
Identifiers:: MONDO: MONDO:0010465; MedGen: C3275495; Orphanet: 2322; OMIM: 300867

Recent activity

Clear Turn Off Turn On

txid3052230[orgn] AND "isolate 211"[All Fields] (113)
SRA
Hepatitis C virus strain 249308 5' UTR, partial sequence
Hepatitis C virus strain 249308 5' UTR, partial sequence
gi|34595155|gb|AY306322.1|

Nucleotide
Hepacivirus hominis envelope protein 2 gene, partial cds.
Hepacivirus hominis envelope protein 2 gene, partial cds.
PopSet: 1229854434

PopSet
txid3052230[orgn] AND "isolate TV386 366d Variant364 freq 0 00046... (1)
txid3052230[orgn] AND "isolate TV386 366d Variant364 freq 0 0004632"[All Fields]
Search

PopSet
Hepacivirus hominis nonstructural protein NS3-4A gene, partial cds.
Hepacivirus hominis nonstructural protein NS3-4A gene, partial cds.
PopSet: 908271548

PopSet

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

Help

Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000255397	UCLA Clinical Genomics Center, UCLA - CES	criteria provided, single submitter (Lee et al. (JAMA. 2014))	Likely pathogenic (Nov 13, 2012)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV001438258	Autoinflammatory diseases unit, CHU de Montpellier	no assertion criteria provided	Pathogenic (Jun 10, 2016)	de novo	clinical testing
SCV002059422	Centogene AG - the Rare Disease Company	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Dec 22, 2018)	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

SCV000255397

UCLA Clinical Genomics Center, UCLA - CES

criteria provided, single submitter

(Lee et al. (JAMA. 2014))

Likely pathogenic
(Nov 13, 2012)

germline

clinical testing

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

SCV001438258

Autoinflammatory diseases unit, CHU de Montpellier

no assertion criteria provided

Pathogenic
(Jun 10, 2016)

de novo

clinical testing

SCV002059422

Centogene AG - the Rare Disease Company

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(Dec 22, 2018)

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	de novo	yes	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing
Ashkenazi Jewish,Irish	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Clinical exome sequencing for genetic identification of rare Mendelian disorders.

Lee H, Deignan JL, Dorrani N, Strom SP, Kantarci S, Quintero-Rivera F, Das K, Toy T, Harry B, Yourshaw M, Fox M, Fogel BL, Martinez-Agosto JA, Wong DA, Chang VY, Shieh PB, Palmer CG, Dipple KM, Grody WW, Vilain E, Nelson SF.

JAMA. 2014 Nov 12;312(18):1880-7. doi: 10.1001/jama.2014.14604.

PubMed [citation]

PMID:: 25326637
PMCID:: PMC4278636

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 UCLA Clinical Genomics Center, UCLA - CES, SCV000255397.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	Ashkenazi Jewish,Irish	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	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Autoinflammatory diseases unit, CHU de Montpellier, SCV001438258.1

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

#	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 Centogene AG - the Rare Disease Company, SCV002059422.1

#	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	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: May 12, 2024

ClinVar

Relating variation to medicine