ClinVar Genomic variation as it relates to human health
NM_015443.4(KANSL1):c.908_909del (p.Lys303fs)
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.
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.
No data submitted for somatic clinical impact
No data submitted for oncogenicity
Variant Details
- Identifiers
-
NM_015443.4(KANSL1):c.908_909del (p.Lys303fs)
Variation ID: 3250486 Accession: VCV003250486.1
- Type and length
-
Deletion, 2 bp
- Location
-
Cytogenetic: 17q21.31 17: 46171235-46171236 (GRCh38) [ NCBI UCSC ] 17: 44248601-44248602 (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 Jul 15, 2024 Jul 15, 2024 Jun 25, 2024 - HGVS
-
Nucleotide Protein Molecular
consequenceNM_015443.4:c.908_909del MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_056258.1:p.Lys303fs frameshift NM_001193465.2:c.908_909del NP_001180394.1:p.Lys303fs frameshift NM_001193466.2:c.908_909del NP_001180395.1:p.Lys303fs frameshift NM_001379198.1:c.908_909del NP_001366127.1:p.Lys303fs frameshift NM_001405854.1:c.908_909del NP_001392783.1:p.Lys303fs frameshift NM_001405855.1:c.908_909del NP_001392784.1:p.Lys303fs frameshift NM_001405856.1:c.908_909del NP_001392785.1:p.Lys303fs frameshift NM_001405857.1:c.908_909del NP_001392786.1:p.Lys303fs frameshift NM_001405858.1:c.908_909del NP_001392787.1:p.Lys303fs frameshift NM_001405859.1:c.908_909del NP_001392788.1:p.Lys303fs frameshift NM_001405860.1:c.908_909del NP_001392789.1:p.Lys303fs frameshift NM_001405861.1:c.908_909del NP_001392790.1:p.Lys303fs frameshift NM_001405872.1:c.908_909del NP_001392801.1:p.Lys303fs frameshift NM_001405873.1:c.908_909del NP_001392802.1:p.Lys303fs frameshift NM_001405874.1:c.908_909del NP_001392803.1:p.Lys303fs frameshift NM_001405875.1:c.908_909del NP_001392804.1:p.Lys303fs frameshift NM_001405876.1:c.908_909del NP_001392805.1:p.Lys303fs frameshift NM_001405877.1:c.908_909del NP_001392806.1:p.Lys303fs frameshift NM_001405878.1:c.908_909del NP_001392807.1:p.Lys303fs frameshift NM_001405879.1:c.908_909del NP_001392808.1:p.Lys303fs frameshift NM_001405880.1:c.908_909del NP_001392809.1:p.Lys303fs frameshift NM_001405881.1:c.908_909del NP_001392810.1:p.Lys303fs frameshift NM_001405882.1:c.23+52435_23+52436del intron variant NM_001405883.1:c.23+52435_23+52436del intron variant NM_001405884.1:c.23+52435_23+52436del intron variant NM_001405885.1:c.23+52435_23+52436del intron variant NC_000017.11:g.46171235_46171236del NC_000017.10:g.44248601_44248602del NG_032784.1:g.59139_59140del - Protein change
- K303fs
- Other names
- -
- Canonical SPDI
- NC_000017.11:46171234:CT:
-
Functional
consequence HelpThe effect of the variant on RNA or protein function, based on experimental evidence from submitters.
-
-
Global minor allele
frequency (GMAF) HelpThe 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
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 | ||
---|---|---|---|---|---|---|
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 |
1222 | 1356 |
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. |
---|---|---|---|---|
Pathogenic (1) |
criteria provided, single submitter
|
Jun 25, 2024 | RCV004585217.1 |
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
(Jun 25, 2024)
|
criteria provided, single submitter
Method: clinical testing
|
Koolen-de Vries syndrome
(Sporadic)
Affected status: yes
Allele origin:
de novo
|
Genomic Medicine, Universita Cattolica del Sacro Cuore
Accession: SCV005061833.1
First in ClinVar: Jul 15, 2024 Last updated: Jul 15, 2024 |
Comment:
De novo frameshift variant in a patient showing the typical Koolen-de Vries syndrome (KdVS) phenotype. Absent from large population studies. It has already been reported … (more)
De novo frameshift variant in a patient showing the typical Koolen-de Vries syndrome (KdVS) phenotype. Absent from large population studies. It has already been reported as causative of KdVS (PMID:26306646). By cDNA analysis, it has been demonstrated that the variant involves the functional full-length KANSL1 gene. NMD is expected to be triggered. IMPORTANT: this variant has been classified as pathogenic in this case because it affects a functional allele of the KANSL1 gene. In theory, it is possible that in other cases it, instead, involves a duplicated genomic region that includes the first two (or three) exons of the KANSL1 transcript NM_015443.4. In such a situation it should be considered benign. It is not possible to define if the variant affects the duplicated region or the functional KANSL1 gene sequence solely on the basis of genomic DNA sequencing results. (less)
Clinical Features:
Global developmental delay (present) , Delayed speech and language development (present) , Generalized hypotonia (present) , Conspicuously happy disposition (present) , High forehead (present) , … (more)
Global developmental delay (present) , Delayed speech and language development (present) , Generalized hypotonia (present) , Conspicuously happy disposition (present) , High forehead (present) , Long face (present) , Prominent nasal bridge (present) , Bulbous nose (present) , Pear-shaped nose (present) , Everted lower lip vermilion (present) (less)
Age: 0-9 years
Sex: male
Geographic origin: Italy
Comment on evidence:
Confirmation of the involvement of the functional full-length KANSL1 gene was obtained by cDNA studies
|
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. |
Citations for germline classification of this variant
HelpThere 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 this variant ...
HelpRecord last updated Jul 23, 2024
This date represents the last time this VCV record was updated. The update may be due to an update to one of the included submitted records (SCVs), or due to an update that ClinVar made to the variant such as adding HGVS expressions or a rs number. So this date may be different from the date of the “most recent submission” reported at the top of this page.