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NM_001193466.2(KANSL1):c.808_809del (p.Leu270fs)

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Interpretation:
Conflicting interpretations of pathogenicity​

Likely pathogenic(1);Pathogenic(2);Uncertain significance(1)

Review status:
criteria provided, conflicting interpretations
Submissions:
4 (Most recent: Jul 4, 2021)
Last evaluated:
Jul 8, 2020
Accession:
VCV000468412.11
Variation ID:
468412
Description:
2bp deletion
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NM_001193466.2(KANSL1):c.808_809del (p.Leu270fs)

Allele ID
468132
Variant type
Deletion
Variant length
2 bp
Cytogenetic location
17q21.31
Genomic location
17: 46171335-46171336 (GRCh38) GRCh38 UCSC
17: 44248701-44248702 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000017.10:g.44248701_44248702del
NC_000017.11:g.46171335_46171336del
NG_032784.1:g.59039_59040del
... more HGVS
Protein change
L270fs
Other names
-
Canonical SPDI
NC_000017.11:46171334:AG:
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
The Genome Aggregation Database (gnomAD), exomes 0.00002
Exome Aggregation Consortium (ExAC) 0.00003
The Genome Aggregation Database (gnomAD) 0.00003
Links
ClinGen: CA8618954
dbSNP: rs551541795
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Pathogenic 1 criteria provided, single submitter Apr 1, 2019 RCV001093449.2
Likely pathogenic 1 criteria provided, single submitter May 3, 2018 RCV001266716.1
Conflicting interpretations of pathogenicity 2 criteria provided, conflicting interpretations Jul 8, 2020 RCV000551044.5

Clinical features observed in individuals with this variant

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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
KANSL1 Sufficient evidence for dosage pathogenicity No evidence available GRCh38
GRCh38
GRCh38
GRCh37
878 1037

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Uncertain significance
(Jul 08, 2020)
criteria provided, single submitter
Method: clinical testing
Koolen-de Vries syndrome
Allele origin: germline
Invitae
Accession: SCV000645070.4
Submitted: (Jan 07, 2021)
Evidence details
Publications
PubMed (4)
Comment:
Due to the possible presence of a polymorphic segmental duplication, the location of the variant could not be unambiguously resolved. If the variant occurs in … (more)
Pathogenic
(Apr 01, 2019)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
CeGaT Praxis fuer Humangenetik Tuebingen
Accession: SCV001250442.6
Submitted: (Jul 04, 2021)
Evidence details
Likely pathogenic
(May 03, 2018)
criteria provided, single submitter
Method: clinical testing
Inborn genetic diseases
Allele origin: germline
Ambry Genetics
Accession: SCV001444893.1
Submitted: (Oct 09, 2020)
Evidence details
Pathogenic
(Sep 28, 2018)
criteria provided, single submitter
Method: clinical testing
Koolen-de Vries syndrome
Allele origin: de novo
Baylor Genetics
Accession: SCV001529643.1
Submitted: (Mar 05, 2021)
Evidence details
Comment:
This variant was determined to be pathogenic according to ACMG Guidelines, 2015 [PMID:25741868].

Functional evidence

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There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Citations for this variant

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Title Author Journal Year Link
Clinically-relevant postzygotic mosaicism in parents and children with developmental disorders in trio exome sequencing data. Wright CF Nature communications 2019 PMID: 31278258
Contribution of next generation sequencing in pediatric practice in Lebanon. A Study on 213 cases. Nair P Molecular genetics & genomic medicine 2018 PMID: 30293248
Mutations in KANSL1 cause the 17q21.31 microdeletion syndrome phenotype. Zollino M Nature genetics 2012 PMID: 22544367
Mutations in the chromatin modifier gene KANSL1 cause the 17q21.31 microdeletion syndrome. Koolen DA Nature genetics 2012 PMID: 22544363

Text-mined citations for rs551541795...

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These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Oct 07, 2021