NM_015443.4(KANSL1):c.611del (p.Gly204fs) AND Koolen-de Vries syndrome

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: Sep 8, 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:: RCV002302484.1

Allele description [Variation Report for NM_015443.4(KANSL1):c.611del (p.Gly204fs)]

NM_015443.4(KANSL1):c.611del (p.Gly204fs)

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.611del (p.Gly204fs)

HGVS:

NC_000017.11:g.46171538del
NG_032784.1:g.58842del
NM_001193465.2:c.611del
NM_001193466.2:c.611del
NM_001379198.1:c.611del
NM_001405854.1:c.606delG
NM_001405855.1:c.606delG
NM_001405856.1:c.606delG
NM_001405857.1:c.606delG
NM_001405858.1:c.606delG
NM_001405859.1:c.606delG
NM_001405860.1:c.606delG
NM_001405861.1:c.606delG
NM_001405872.1:c.606delG
NM_001405873.1:c.606delG
NM_001405874.1:c.606delG
NM_001405875.1:c.606delG
NM_001405876.1:c.606delG
NM_001405877.1:c.606delG
NM_001405878.1:c.606delG
NM_001405879.1:c.606delG
NM_001405880.1:c.606delG
NM_001405881.1:c.606delG
NM_015443.4:c.611delMANE SELECT
NP_001180394.1:p.Gly204fs
NP_001180395.1:p.Gly204fs
NP_001366127.1:p.Gly204fs
NP_001392783.1:p.Gly204Valfs
NP_001392784.1:p.Gly204Valfs
NP_001392785.1:p.Gly204Valfs
NP_001392786.1:p.Gly204Valfs
NP_001392787.1:p.Gly204Valfs
NP_001392788.1:p.Gly204Valfs
NP_001392789.1:p.Gly204Valfs
NP_001392790.1:p.Gly204Valfs
NP_001392801.1:p.Gly204Valfs
NP_001392802.1:p.Gly204Valfs
NP_001392803.1:p.Gly204Valfs
NP_001392804.1:p.Gly204Valfs
NP_001392805.1:p.Gly204Valfs
NP_001392806.1:p.Gly204Valfs
NP_001392807.1:p.Gly204Valfs
NP_001392808.1:p.Gly204Valfs
NP_001392809.1:p.Gly204Valfs
NP_001392810.1:p.Gly204Valfs
NP_056258.1:p.Gly204fs
NC_000017.10:g.44248904del
NM_001193466.1:c.611delG

Protein change:

G204fs

Molecular consequence:

NM_001193465.2:c.611del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001193466.2:c.611del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001379198.1:c.611del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001405854.1:c.606delG - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001405855.1:c.606delG - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001405856.1:c.606delG - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001405857.1:c.606delG - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001405858.1:c.606delG - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001405859.1:c.606delG - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001405860.1:c.606delG - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001405861.1:c.606delG - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001405872.1:c.606delG - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001405873.1:c.606delG - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001405874.1:c.606delG - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001405875.1:c.606delG - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001405876.1:c.606delG - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001405877.1:c.606delG - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001405878.1:c.606delG - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001405879.1:c.606delG - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001405880.1:c.606delG - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001405881.1:c.606delG - frameshift variant - [Sequence Ontology: SO:0001589]
NM_015443.4:c.611del - 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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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002598702	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	criteria provided, single submitter (LabCorp Variant Classification Summary - May 2015)	Likely pathogenic (Sep 8, 2022)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002598702

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)

Likely pathogenic
(Sep 8, 2022)

germline

clinical testing

Citation Link

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

Details of each submission

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV002598702.1

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

Description

Variant summary: KIAA1267 (also known as KANSL1) c.611delG (p.Gly204ValfsX2) results in a premature termination codon, predicted to cause a truncation of the encoded protein or absence of the protein due to nonsense mediated decay, which are commonly known mechanisms for disease. Truncations downstream of this position have been classified as pathogenic in ClinVar database. The variant was absent in 250078 control chromosomes (gnomAD). To our knowledge, no occurrence of c.611delG in individuals affected with Koolen-De Vries Syndrome and no experimental evidence demonstrating its impact on protein function have been reported. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014. Based on the evidence outlined above, the variant was classified as likely 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: Nov 13, 2022

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