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NM_001193466.2(KANSL1):c.19G>A (p.Ala7Thr)

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Interpretation:
Conflicting interpretations of pathogenicity​

Likely benign(2);Uncertain significance(1)

Review status:
criteria provided, conflicting interpretations
Submissions:
3 (Most recent: Jan 7, 2021)
Last evaluated:
Oct 9, 2018
Accession:
VCV000205802.4
Variation ID:
205802
Description:
single nucleotide variant
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NM_001193466.2(KANSL1):c.19G>A (p.Ala7Thr)

Allele ID
203452
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
17q21.31
Genomic location
17: 46172125 (GRCh38) GRCh38 UCSC
17: 44249491 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000017.11:g.46172125C>T
NC_000017.10:g.44249491C>T
NM_001193465.1:c.19G>A NP_001180394.1:p.Ala7Thr missense
... more HGVS
Protein change
A7T
Other names
p.A7T:GCT>ACT
Canonical SPDI
NC_000017.11:46172124:C:T
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
Exome Aggregation Consortium (ExAC) 0.00002
Links
ClinGen: CA315231
dbSNP: rs768152581
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Likely benign 1 criteria provided, single submitter Oct 5, 2018 RCV001497152.1
Conflicting interpretations of pathogenicity 2 criteria provided, conflicting interpretations Oct 9, 2018 RCV000187790.3
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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
(Mar 17, 2014)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV000241387.11
Submitted: (Jan 29, 2019)
Evidence details
Comment:
This variant is denoted p.Ala7Thr (GCT>ACT): c.19 G>A in exon 2 of the KANSL1 gene (NM_001193466.1). The A7T variant has not been published as a … (more)
Likely benign
(Oct 09, 2018)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Invitae
Accession: SCV000831576.2
Submitted: (Mar 14, 2019)
Evidence details
Publications
PubMed (1)
Likely benign
(Oct 05, 2018)
criteria provided, single submitter
Method: clinical testing
Koolen-de Vries syndrome
Allele origin: germline
Invitae
Accession: SCV001701871.1
Submitted: (Jan 07, 2021)
Evidence details

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
Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria. Nykamp K Genetics in medicine : official journal of the American College of Medical Genetics 2017 PMID: 28492532

Text-mined citations for rs768152581...

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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 Jun 14, 2021