ClinVar Genomic variation as it relates to human health
NM_001174096.2(ZEB1):c.862dup (p.Ile288fs)
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
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NM_001174096.2(ZEB1):c.862dup (p.Ile288fs)
Variation ID: 2694368 Accession: VCV002694368.1
- Type and length
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Duplication, 1 bp
- Location
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Cytogenetic: 10p11.22 10: 31520193-31520194 (GRCh38) [ NCBI UCSC ] 10: 31809121-31809122 (GRCh37) [ NCBI UCSC ]
- Timeline in ClinVar
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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 Feb 14, 2024 Feb 14, 2024 Nov 8, 2023 - HGVS
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Nucleotide Protein Molecular
consequenceNM_001174096.2:c.862dup MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_001167567.1:p.Ile288fs frameshift NM_001128128.3:c.811dup NP_001121600.1:p.Ile271fs frameshift NM_001174093.2:c.799dup NP_001167564.1:p.Ile267fs frameshift NM_001174094.2:c.808dup NP_001167565.1:p.Ile270fs frameshift NM_001174095.2:c.658dup NP_001167566.1:p.Ile220fs frameshift NM_001323638.2:c.205dup NP_001310567.1:p.Ile69fs frameshift NM_001323641.2:c.205dup NP_001310570.1:p.Ile69fs frameshift NM_001323642.2:c.205dup NP_001310571.1:p.Ile69fs frameshift NM_001323643.2:c.205dup NP_001310572.1:p.Ile69fs frameshift NM_001323644.2:c.205dup NP_001310573.1:p.Ile69fs frameshift NM_001323645.2:c.205dup NP_001310574.1:p.Ile69fs frameshift NM_001323646.2:c.205dup NP_001310575.1:p.Ile69fs frameshift NM_001323647.2:c.205dup NP_001310576.1:p.Ile69fs frameshift NM_001323648.2:c.205dup NP_001310577.1:p.Ile69fs frameshift NM_001323649.2:c.205dup NP_001310578.1:p.Ile69fs frameshift NM_001323650.2:c.205dup NP_001310579.1:p.Ile69fs frameshift NM_001323651.2:c.205dup NP_001310580.1:p.Ile69fs frameshift NM_001323652.2:c.205dup NP_001310581.1:p.Ile69fs frameshift NM_001323653.2:c.205dup NP_001310582.1:p.Ile69fs frameshift NM_001323654.2:c.205dup NP_001310583.1:p.Ile69fs frameshift NM_001323655.2:c.205dup NP_001310584.1:p.Ile69fs frameshift NM_001323656.2:c.205dup NP_001310585.1:p.Ile69fs frameshift NM_001323657.2:c.205dup NP_001310586.1:p.Ile69fs frameshift NM_001323658.2:c.205dup NP_001310587.1:p.Ile69fs frameshift NM_001323659.2:c.205dup NP_001310588.1:p.Ile69fs frameshift NM_001323660.2:c.205dup NP_001310589.1:p.Ile69fs frameshift NM_001323661.2:c.205dup NP_001310590.1:p.Ile69fs frameshift NM_001323662.2:c.205dup NP_001310591.1:p.Ile69fs frameshift NM_001323663.2:c.205dup NP_001310592.1:p.Ile69fs frameshift NM_001323664.2:c.205dup NP_001310593.1:p.Ile69fs frameshift NM_001323665.2:c.205dup NP_001310594.1:p.Ile69fs frameshift NM_001323666.2:c.205dup NP_001310595.1:p.Ile69fs frameshift NM_001323671.2:c.205dup NP_001310600.1:p.Ile69fs frameshift NM_001323672.2:c.205dup NP_001310601.1:p.Ile69fs frameshift NM_001323673.2:c.205dup NP_001310602.1:p.Ile69fs frameshift NM_001323674.2:c.637dup NP_001310603.1:p.Ile213fs frameshift NM_001323675.2:c.595dup NP_001310604.1:p.Ile199fs frameshift NM_001323676.2:c.820dup NP_001310605.1:p.Ile274fs frameshift NM_001323677.2:c.817dup NP_001310606.1:p.Ile273fs frameshift NM_001323678.2:c.586dup NP_001310607.1:p.Ile196fs frameshift NM_030751.6:c.859dup NP_110378.3:p.Ile287fs frameshift NR_024285.1:n.1572dup NR_024286.1:n.1117dup NR_024287.1:n.1454dup NC_000010.11:g.31520194dup NC_000010.10:g.31809122dup NG_017048.1:g.206022dup NG_017048.2:g.206779dup - Protein change
- I196fs, I213fs, I271fs, I274fs, I287fs, I288fs, I69fs, I267fs, I199fs, I220fs, I273fs, I270fs
- Other names
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- Canonical SPDI
- NC_000010.11:31520193:A:AA
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Functional
consequence HelpThe effect of the variant on RNA or protein function, based on experimental evidence from submitters.
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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.
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Allele frequency
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The frequency of the allele represented by this VCV record.
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- Links
Genes
Gene | OMIM | ClinGen Gene Dosage Sensitivity Curation |
Variation Viewer
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Links to Variation Viewer, a genome browser to view variation data from NCBI databases. |
Related variants | ||
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HI score
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The haploinsufficiency score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
TS score
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The triplosensitivity score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
Within gene
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The number of variants in ClinVar that are contained within this gene, with a link to view the list of variants. |
All
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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. |
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ZEB1 | - | - |
GRCh38 GRCh37 |
122 | 140 |
Conditions - Germline
Condition
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The condition for this variant-condition (RCV) record in ClinVar. |
Classification
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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
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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
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The most recent date that a submitter evaluated this variant for the condition. |
Variation/condition record
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The RCV accession number, with most recent version number, for the variant-condition record, with a link to the RCV web page. |
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Pathogenic (1) |
criteria provided, single submitter
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Nov 8, 2023 | RCV003544114.1 |
Submissions - Germline
Classification
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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
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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
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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
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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. |
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Pathogenic
(Nov 08, 2023)
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criteria provided, single submitter
Method: clinical testing
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not provided
Affected status: unknown
Allele origin:
germline
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Invitae
Accession: SCV004249299.1
First in ClinVar: Feb 14, 2024 Last updated: Feb 14, 2024 |
Comment:
This sequence change creates a premature translational stop signal (p.Ile287Asnfs*4) in the ZEB1 gene. It is expected to result in an absent or disrupted protein … (more)
This sequence change creates a premature translational stop signal (p.Ile287Asnfs*4) in the ZEB1 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in ZEB1 are known to be pathogenic (PMID: 16252232, 17935237, 30851240). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with ZEB1-related conditions. For these reasons, this variant has been classified as Pathogenic. (less)
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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
HelpTitle | Author | Journal | Year | Link |
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The utility of massively parallel sequencing for posterior polymorphous corneal dystrophy type 3 molecular diagnosis. | Dudakova L | Experimental eye research | 2019 | PMID: 30851240 |
Posterior polymorphous corneal dystrophy is associated with TCF8 gene mutations and abdominal hernia. | Aldave AJ | American journal of medical genetics. Part A | 2007 | PMID: 17935237 |
Mutations in TCF8 cause posterior polymorphous corneal dystrophy and ectopic expression of COL4A3 by corneal endothelial cells. | Krafchak CM | American journal of human genetics | 2005 | PMID: 16252232 |
Text-mined citations for this variant ...
HelpRecord last updated Feb 20, 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.