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NM_015443.4(KANSL1):c.2591del (p.Asn864fs) AND Koolen-de Vries syndrome

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Jun 17, 2019
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
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:
RCV001253770.1

Allele description

NM_015443.4(KANSL1):c.2591del (p.Asn864fs)

Gene:
KANSL1:KAT8 regulatory NSL complex subunit 1 [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
17q21.31
Genomic location:
Preferred name:
NM_015443.4(KANSL1):c.2591del (p.Asn864fs)
HGVS:
  • NC_000017.11:g.46034237del
  • NG_032784.1:g.196139del
  • NM_001193465.2:c.2588del
  • NM_001193466.2:c.2591del
  • NM_001379198.1:c.2591del
  • NM_015443.4:c.2591delMANE SELECT
  • NP_001180394.1:p.Asn863fs
  • NP_001180395.1:p.Asn864fs
  • NP_001366127.1:p.Asn864fs
  • NP_056258.1:p.Asn864fs
  • NC_000017.10:g.44111603del
  • NM_001193466.1:c.2591delA
  • p.Asn864Thrfs*14
Protein change:
N863fs
Links:
dbSNP: rs2077088526
NCBI 1000 Genomes Browser:
rs2077088526
Molecular consequence:
  • NM_001193465.2:c.2588del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001193466.2:c.2591del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001379198.1:c.2591del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_015443.4:c.2591del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Name:
Koolen-de Vries syndrome (KDVS)
Synonyms:
KANSL1-Related Intellectual Disability Syndrome
Identifiers:
MONDO: MONDO:0012496; MedGen: C1864871; Orphanet: 96169; OMIM: 610443

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001427062Clinical Genomics Program, Stanford Medicine
no assertion criteria provided
Pathogenic
(Jun 17, 2019) 		germlineclinical testing

Help

Summary from all submissions

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

Details of each submission

From Clinical Genomics Program, Stanford Medicine, SCV001427062.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providedclinical testingnot provided

Description

The p.Asn864Thrfs*14 variant in the KANSL1 gene was identified de novo in this individual but has not been previously reported in association with disease. This variant was absent from large population databases, including the Genome Aggregation Database (http://gnomad.broadinstitute.org/). The p.Asn864Thrfs*14 variant results in a 1bp deletion, which causes a shift in the protein reading frame, leading to a premature termination codon 14 amino acids downstream. Heterozygous loss of function is an established mechanism of disease for the KANSL1 gene. These data were assessed using the ACMG/AMP variant interpretation guidelines. In summary, there is sufficient evidence to classify the p.Asn864Thrfs*14 variant as pathogenic for autosomal dominant KANSL1-related intellectual disability syndrome based on the information above. [ACMG evidence codes used: PVS1; PS2_moderate; PM2].

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

Last Updated: Jun 3, 2022