NC_000023.10:g.(?_43515590)_(44970656_?)del AND Kabuki syndrome 2

This record was updated by the submitter. Please see the current version.

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Aug 31, 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:: RCV003109821.2

Allele description

NC_000023.10:g.(?_43515590)_(44970656_?)del

Genes:

EFHC2:EF-hand domain containing 2 [Gene - OMIM - HGNC]
FUNDC1:FUN14 domain containing 1 [Gene - OMIM - HGNC]
DUSP21:dual specificity phosphatase 21 [Gene - OMIM - HGNC]
KDM6A:lysine demethylase 6A [Gene - OMIM - HGNC]
MAOA:monoamine oxidase A [Gene - OMIM - HGNC]
MAOB:monoamine oxidase B [Gene - OMIM - HGNC]
NDP:norrin cystine knot growth factor NDP [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

Xp11.3

Genomic location:

ChrX: 43515590 - 44970656 (on Assembly GRCh37)

Preferred name:

NC_000023.10:g.(?_43515590)_(44970656_?)del

HGVS:

NC_000023.10:g.(?_43515590)_(44970656_?)del

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
SCV003791824	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Aug 31, 2022)	germline	clinical testing	PubMed (6) [See all records that cite these PMIDs] 23076834, 23913813, 22197486, 23354975, 25972376, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003791824

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Aug 31, 2022)

germline

clinical testing

PubMed (6)
[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	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

KDM6A point mutations cause Kabuki syndrome.

Miyake N, Mizuno S, Okamoto N, Ohashi H, Shiina M, Ogata K, Tsurusaki Y, Nakashima M, Saitsu H, Niikawa N, Matsumoto N.

Hum Mutat. 2013 Jan;34(1):108-10. doi: 10.1002/humu.22229. Epub 2012 Oct 17.

PubMed [citation]

PMID:: 23076834

MLL2 and KDM6A mutations in patients with Kabuki syndrome.

Miyake N, Koshimizu E, Okamoto N, Mizuno S, Ogata T, Nagai T, Kosho T, Ohashi H, Kato M, Sasaki G, Mabe H, Watanabe Y, Yoshino M, Matsuishi T, Takanashi J, Shotelersuk V, Tekin M, Ochi N, Kubota M, Ito N, Ihara K, Hara T, et al.

Am J Med Genet A. 2013 Sep;161A(9):2234-43. doi: 10.1002/ajmg.a.36072. Epub 2013 Aug 2.

PubMed [citation]

PMID:: 23913813

See all PubMed Citations (6)

Details of each submission

From Invitae, SCV003791824.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (6)

Description

A gross deletion of the genomic region encompassing the full coding sequence of the KDM6A gene has been identified. Loss-of-function variants in KDM6A are known to be pathogenic (PMID: 23076834, 23913813). The boundaries of this event are unknown as they extend beyond the assayed region for this gene and therefore may encompass additional genes. Isolated whole-gene deletions of KDM6A have not been reported in the literature. However, larger copy number events that include this gene have been reported (PMID: 22197486, 23354975, 25972376). For these reasons, this variant has been classified as Pathogenic.

#	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: Feb 18, 2023

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