VCV000419679.1 - ClinVar

NM_015443.4(KANSL1):c.536_537dup (p.Lys180fs)

Germline

Classification

The aggregate germline classification for this variant, typically for a monogenic or Mendelian disorder as in the ACMG/AMP guidelines, or for response to a drug. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the aggregate classification.

(1)

Stars represent the aggregate review status, or the level of review supporting the aggregate germline classification for this VCV record. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. The number of submissions which contribute to this review status is shown in parentheses.

Pathogenic

criteria provided, single submitter

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

Identifiers

NM_015443.4(KANSL1):c.536_537dup (p.Lys180fs)

Variation ID: 419679 Accession: VCV000419679.1

Type and length

Duplication, 2 bp

Location

Cytogenetic: 17q21.31 17: 46171606-46171607 (GRCh38) [ NCBI UCSC ] 17: 44248972-44248973 (GRCh37) [ NCBI UCSC ]

Timeline in ClinVar

	First in ClinVar Help The date this variant first appeared in ClinVar with each type of classification.	Last submission Help The date of the most recent submission for each type of classification for this variant.	Last evaluated Help The most recent date that a submitter evaluated this variant for each type of classification.
Germline	Apr 27, 2017	Apr 27, 2017	Aug 5, 2015

HGVS

Nucleotide	Protein	Molecular consequence
NM_015443.4:c.536_537dup MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.	NP_056258.1:p.Lys180fs	frameshift
NM_001193465.2:c.536_537dup	NP_001180394.1:p.Lys180fs	frameshift
NM_001193466.2:c.536_537dup	NP_001180395.1:p.Lys180fs	frameshift
NM_001379198.1:c.536_537dup	NP_001366127.1:p.Lys180fs	frameshift
NC_000017.11:g.46171607_46171608dup
NC_000017.10:g.44248973_44248974dup
NG_032784.1:g.58767_58768dup

... more HGVS ... less HGVS

Protein change

K180fs

Other names

Canonical SPDI

NC_000017.11:46171606:TC:TCTC

Functional consequence Help The effect of the variant on RNA or protein function, based on experimental evidence from submitters.

Global minor allele frequency (GMAF) Help The global minor allele frequency calculated by the 1000 Genomes Project. The minor allele at this location is indicated in parentheses and may be different from the allele represented by this VCV record.

Allele frequency Help The frequency of the allele represented by this VCV record.

Links

ClinGen: CA16620461 dbSNP: rs1064794038 VarSome

Genes

Gene	OMIM	ClinGen Gene Dosage Sensitivity Curation		Variation Viewer Help Links to Variation Viewer, a genome browser to view variation data from NCBI databases.	Related variants
Gene	OMIM	HI score Help The haploinsufficiency score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team.	TS score Help The triplosensitivity score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team.		Within gene Help The number of variants in ClinVar that are contained within this gene, with a link to view the list of variants.	All Help The number of variants in ClinVar for this gene, including smaller variants within the gene and larger CNVs that overlap or fully contain the gene.
KANSL1		Sufficient evidence for dosage pathogenicity	No evidence available	GRCh38 GRCh38 GRCh38 GRCh37	1244	1381

Conditions - Germline

Condition Help The condition for this variant-condition (RCV) record in ClinVar.	Classification Help The aggregate germline classification for this variant-condition (RCV) record in ClinVar. The number of submissions that contribute to this aggregate classification is shown in parentheses. (# of submissions)	Review status Help The aggregate review status for this variant-condition (RCV) record in ClinVar. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status.	Last evaluated Help The most recent date that a submitter evaluated this variant for the condition.	Variation/condition record Help The RCV accession number, with most recent version number, for the variant-condition record, with a link to the RCV web page.
not provided	Pathogenic (1)	criteria provided, single submitter	Aug 5, 2015	RCV000484111.1

Submissions - Germline

Classification Help The submitted germline classification for each SCV record. (Last evaluated)	Review status Help Stars represent the review status, or the level of review supporting the submitted (SCV) record. This value is calculated by NCBI based on data from the submitter. Read our rules for calculating the review status. This column also includes a link to the submitter’s assertion criteria if provided, and the collection method. (Assertion criteria)	Condition Help The condition for the classification, provided by the submitter for this submitted (SCV) record. This column also includes the affected status and allele origin of individuals observed with this variant.	Submitter Help The submitting organization for this submitted (SCV) record. This column also includes the SCV accession and version number, the date this SCV first appeared in ClinVar, and the date that this SCV was last updated in ClinVar.	More information Help This column includes more information supporting the classification, including citations, the comment on classification, and detailed evidence provided as observations of the variant by the submitter.
Pathogenic (Aug 05, 2015)	criteria provided, single submitter (GeneDx Variant Classification (06012015)) Method: clinical testing	Not Provided Affected status: yes Allele origin: germline	GeneDx Accession: SCV000567647.3 First in ClinVar: Apr 27, 2017 Last updated: Apr 27, 2017	Comment: The c.536_537dupGA duplication in the KANSL1 gene has not been reported previously as a pathogenic variant nor as a benign polymorphism, to our knowledge. The … (more) The c.536_537dupGA duplication in the KANSL1 gene has not been reported previously as a pathogenic variant nor as a benign polymorphism, to our knowledge. The c.536_537dupGA variant causes a frameshift starting with codon Lysine 180 changes this amino acid to a Glutamic acid residue, and creates a premature Stop codon at position 23 of the new reading frame, denoted p.Lys180GlufsX23. This duplication is predicted to cause loss of normal protein function either through protein truncation or nonsense-mediated mRNA decay. The c.536_537dupGA variant was not observed in approximately 6500 individuals of European and African American ancestry in the NHLBI Exome Sequencing Project, indicating it is not a common benign variant in these populations. We interpret c.536_537dupGA as a pathogenic variant. (less)

Comment:

The c.536_537dupGA duplication in the KANSL1 gene has not been reported previously as a pathogenic variant nor as a benign polymorphism, to our knowledge. The c.536_537dupGA variant causes a frameshift starting with codon Lysine 180 changes this amino acid to a Glutamic acid residue, and creates a premature Stop codon at position 23 of the new reading frame, denoted p.Lys180GlufsX23. This duplication is predicted to cause loss of normal protein function either through protein truncation or nonsense-mediated mRNA decay. The c.536_537dupGA variant was not observed in approximately 6500 individuals of European and African American ancestry in the NHLBI Exome Sequencing Project, indicating it is not a common benign variant in these populations. We interpret c.536_537dupGA as a pathogenic variant.

Germline Functional Evidence

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.

Comment:

Citations for germline classification of this variant

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

Text-mined citations for rs1064794038 ...

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 Apr 25, 2022

ClinVar Genomic variation as it relates to human health

NM_015443.4(KANSL1):c.536_537dup (p.Lys180fs)

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for rs1064794038 ...