NM_001291415.2(KDM6A):c.2597_2598del (p.Ser866fs) AND Kabuki syndrome 2

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Feb 1, 2022
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:: RCV002245292.2

Allele description [Variation Report for NM_001291415.2(KDM6A):c.2597_2598del (p.Ser866fs)]

NM_001291415.2(KDM6A):c.2597_2598del (p.Ser866fs)

Gene:

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

Variant type:

Microsatellite

Cytogenetic location:

Xp11.3

Genomic location:

Preferred name:

NM_001291415.2(KDM6A):c.2597_2598del (p.Ser866fs)

HGVS:

NC_000023.11:g.45070094CT[1]
NG_016260.1:g.201917CT[1]
NM_001291415.2:c.2597_2598delMANE SELECT
NM_001291416.2:c.2462_2463del
NM_001291417.2:c.2306_2307del
NM_001291418.2:c.2204_2205del
NM_001291421.2:c.1553_1554del
NM_021140.4:c.2441_2442del
NP_001278344.1:p.Ser866fs
NP_001278345.1:p.Ser821fs
NP_001278346.1:p.Ser769fs
NP_001278347.1:p.Ser735fs
NP_001278350.1:p.Ser518fs
NP_066963.2:p.Ser814fs
LRG_616:g.201917CT[1]
NC_000023.10:g.44929339CT[1]
NR_111960.2:n.2722CT[1]

Protein change:

S518fs

Links:

dbSNP: rs2148050812

NCBI 1000 Genomes Browser:

rs2148050812

Molecular consequence:

NM_001291415.2:c.2597_2598del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001291416.2:c.2462_2463del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001291417.2:c.2306_2307del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001291418.2:c.2204_2205del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001291421.2:c.1553_1554del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_021140.4:c.2441_2442del - frameshift variant - [Sequence Ontology: SO:0001589]
NR_111960.2:n.2722CT[1] - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Observations:

Condition(s)

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

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002515341	Daryl Scott Lab, Baylor College of Medicine	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Feb 1, 2022)	de novo	clinical testing	PubMed (2) [See all records that cite these PMIDs] 25741868, 36474027

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002515341

Daryl Scott Lab, Baylor College of Medicine

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(Feb 1, 2022)

de novo

clinical testing

PubMed (2)
[See all records that cite these PMIDs]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	de novo	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

High molecular diagnostic yields and novel phenotypic expansions involving syndromic anorectal malformations.

Belanger Deloge R, Zhao X, Luna PN, Shaw CA, Rosenfeld JA, Scott DA.

Eur J Hum Genet. 2023 Mar;31(3):296-303. doi: 10.1038/s41431-022-01255-y. Epub 2022 Dec 6.

PubMed [citation]

PMID:: 36474027
PMCID:: PMC9995493

Details of each submission

From Daryl Scott Lab, Baylor College of Medicine, SCV002515341.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	1	not provided	not provided	clinical testing	PubMed (2)

#	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		1	not provided	not provided	not provided

Last Updated: Jul 29, 2024

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