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NM_006766.5(KAT6A):c.4980del (p.Gln1660fs) AND Autosomal dominant intellectual disability-craniofacial anomalies-cardiac defects syndrome

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Aug 5, 2021
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:
RCV003985159.1

Allele description [Variation Report for NM_006766.5(KAT6A):c.4980del (p.Gln1660fs)]

NM_006766.5(KAT6A):c.4980del (p.Gln1660fs)

Gene:
KAT6A:lysine acetyltransferase 6A [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
8p11.21
Genomic location:
Preferred name:
NM_006766.5(KAT6A):c.4980del (p.Gln1660fs)
HGVS:
  • NC_000008.11:g.41933240del
  • NG_042093.1:g.123787del
  • NM_006766.5:c.4980delMANE SELECT
  • NP_006757.2:p.Gln1660fs
  • NC_000008.10:g.41790758del
Protein change:
Q1660fs
Molecular consequence:
  • NM_006766.5:c.4980del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Name:
Autosomal dominant intellectual disability-craniofacial anomalies-cardiac defects syndrome (ARTHS)
Synonyms:
Arboleda-Tham syndrome; Mental retardation, autosomal dominant 32; KAT6A syndrome
Identifiers:
MONDO: MONDO:0014558; MedGen: C4225396; Orphanet: 457193; OMIM: 616268

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV004801461Illumina Laboratory Services, Illumina
criteria provided, single submitter

(ICSLVariantClassificationCriteria RUGD 01 April 2020)		Pathogenic
(Aug 5, 2021) 		unknownclinical testing

Citation Link

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Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedunknownunknownnot providednot providednot providednot providednot providedclinical testing

Details of each submission

From Illumina Laboratory Services, Illumina, SCV004801461.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

The KAT6A c.4980delG p.(Gln1660HisfsTer48) causes a shift in the protein reading frame that is predicted to result in premature termination of the protein. This variant occurs in the last exon of the gene and the resulting transcript may escape nonsense-mediated mRNA decay (Kennedy et al. 2018). To our knowledge, this variant has not been reported in the peer-reviewed literature. This variant is not observed in version 2.1.1 or version 3.1.2 of the Genome Aggregation Database. This variant is predicted to disrupt the C-terminal serine/methionine rich domain of the protein, which is known to interact with several transcription factors including Runx2 (Wiesel-Motiuk et al. 2020). The variant was identified in a de novo state in the proband. Based on the collective evidence, the c.4980delG p.(Gln1660HisfsTer48) variant it is classified as pathogenic for KAT6A syndrome.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Jun 23, 2024