Skip to main page content
Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation

ClinVar Genomic variation as it relates to human health

Advanced search

NM_001193466.2(KANSL1):c.1826G>A (p.Ser609Asn)

Help
Interpretation:
Conflicting interpretations of pathogenicity​

Benign(3);Likely benign(1);Uncertain significance(1)

Review status:
criteria provided, conflicting interpretations
Submissions:
5 (Most recent: Sep 14, 2021)
Last evaluated:
Dec 5, 2020
Accession:
VCV000376914.7
Variation ID:
376914
Description:
single nucleotide variant
Help

NM_001193466.2(KANSL1):c.1826G>A (p.Ser609Asn)

Allele ID
363792
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
17q21.31
Genomic location
17: 46066559 (GRCh38) GRCh38 UCSC
17: 44143925 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000017.10:g.44143925C>T
NC_000017.11:g.46066559C>T
NG_032784.1:g.163816G>A
... more HGVS
Protein change
S609N
Other names
-
Canonical SPDI
NC_000017.11:46066558:C:T
Functional consequence
-
Global minor allele frequency (GMAF)
0.00220 (T)

Allele frequency
The Genome Aggregation Database (gnomAD), exomes 0.00048
Trans-Omics for Precision Medicine (TOPMed) 0.00168
1000 Genomes Project 0.00220
Exome Aggregation Consortium (ExAC) 0.00056
The Genome Aggregation Database (gnomAD) 0.00146
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00177
Links
ClinGen: CA8618721
dbSNP: rs138698439
Varsome
Help

Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Benign/Likely benign 3 criteria provided, multiple submitters, no conflicts May 31, 2019 RCV000438080.5
Conflicting interpretations of pathogenicity 2 criteria provided, conflicting interpretations Dec 5, 2020 RCV000474219.7
Help
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
860 1019

Submitted interpretations and evidence

Help
Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Benign
(May 31, 2019)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Athena Diagnostics Inc
Accession: SCV001144289.1
Submitted: (Sep 25, 2019)
Evidence details
Benign
(Mar 03, 2015)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV001861340.1
Submitted: (Sep 14, 2021)
Evidence details
Comment:
This variant is associated with the following publications: (PMID: 30924900)
Likely Benign
(Nov 22, 2016)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Center for Pediatric Genomic Medicine,Children's Mercy Hospital and Clinics
Accession: SCV000510863.1
Submitted: (Feb 17, 2017)
Evidence details
Comment:
Converted during submission to Likely benign.
Uncertain significance
(Oct 11, 2017)
criteria provided, single submitter
Method: clinical testing
Koolen-de Vries syndrome
Allele origin: germline
Center for Genomics, Ann and Robert H. Lurie Children's Hospital of Chicago
Accession: SCV000898763.1
Submitted: (Dec 12, 2018)
Evidence details
Comment:
KANSL1 NM_001193466.1 exon 6 p.Ser609Asn (c.1826G>A): This variant has not been reported in the literature but is present in 0.4% (115/24030) of African alleles in … (more)
Benign
(Dec 05, 2020)
criteria provided, single submitter
Method: clinical testing
Koolen-de Vries syndrome
Allele origin: germline
Invitae
Accession: SCV000559733.6
Submitted: (Jan 07, 2021)
Evidence details

Functional evidence

Help
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

Help
There are no citations in ClinVar for this variation. If you know of citations for this variation, please consider submitting that information to ClinVar.

Text-mined citations for rs138698439...

Help
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 Sep 18, 2021