ClinVar Genomic variation as it relates to human health
NM_001174096.2(ZEB1):c.1972A>T (p.Lys658Ter)
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.1972A>T (p.Lys658Ter)
Variation ID: 2853981 Accession: VCV002853981.1
- Type and length
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single nucleotide variant, 1 bp
- Location
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Cytogenetic: 10p11.22 10: 31521304 (GRCh38) [ NCBI UCSC ] 10: 31810232 (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 20, 2024 Feb 20, 2024 Apr 9, 2023 - HGVS
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Nucleotide Protein Molecular
consequenceNM_001174096.2:c.1972A>T MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_001167567.1:p.Lys658Ter nonsense NM_001128128.3:c.1921A>T NP_001121600.1:p.Lys641Ter nonsense NM_001174093.2:c.1909A>T NP_001167564.1:p.Lys637Ter nonsense NM_001174094.2:c.1918A>T NP_001167565.1:p.Lys640Ter nonsense NM_001174095.2:c.1768A>T NP_001167566.1:p.Lys590Ter nonsense NM_001323638.2:c.1315A>T NP_001310567.1:p.Lys439Ter nonsense NM_001323641.2:c.1315A>T NP_001310570.1:p.Lys439Ter nonsense NM_001323642.2:c.1315A>T NP_001310571.1:p.Lys439Ter nonsense NM_001323643.2:c.1315A>T NP_001310572.1:p.Lys439Ter nonsense NM_001323644.2:c.1315A>T NP_001310573.1:p.Lys439Ter nonsense NM_001323645.2:c.1315A>T NP_001310574.1:p.Lys439Ter nonsense NM_001323646.2:c.1315A>T NP_001310575.1:p.Lys439Ter nonsense NM_001323647.2:c.1315A>T NP_001310576.1:p.Lys439Ter nonsense NM_001323648.2:c.1315A>T NP_001310577.1:p.Lys439Ter nonsense NM_001323649.2:c.1315A>T NP_001310578.1:p.Lys439Ter nonsense NM_001323650.2:c.1315A>T NP_001310579.1:p.Lys439Ter nonsense NM_001323651.2:c.1315A>T NP_001310580.1:p.Lys439Ter nonsense NM_001323652.2:c.1315A>T NP_001310581.1:p.Lys439Ter nonsense NM_001323653.2:c.1315A>T NP_001310582.1:p.Lys439Ter nonsense NM_001323654.2:c.1315A>T NP_001310583.1:p.Lys439Ter nonsense NM_001323655.2:c.1315A>T NP_001310584.1:p.Lys439Ter nonsense NM_001323656.2:c.1315A>T NP_001310585.1:p.Lys439Ter nonsense NM_001323657.2:c.1315A>T NP_001310586.1:p.Lys439Ter nonsense NM_001323658.2:c.1315A>T NP_001310587.1:p.Lys439Ter nonsense NM_001323659.2:c.1315A>T NP_001310588.1:p.Lys439Ter nonsense NM_001323660.2:c.1315A>T NP_001310589.1:p.Lys439Ter nonsense NM_001323661.2:c.1315A>T NP_001310590.1:p.Lys439Ter nonsense NM_001323662.2:c.1315A>T NP_001310591.1:p.Lys439Ter nonsense NM_001323663.2:c.1315A>T NP_001310592.1:p.Lys439Ter nonsense NM_001323664.2:c.1315A>T NP_001310593.1:p.Lys439Ter nonsense NM_001323665.2:c.1315A>T NP_001310594.1:p.Lys439Ter nonsense NM_001323666.2:c.1315A>T NP_001310595.1:p.Lys439Ter nonsense NM_001323671.2:c.1315A>T NP_001310600.1:p.Lys439Ter nonsense NM_001323672.2:c.1315A>T NP_001310601.1:p.Lys439Ter nonsense NM_001323673.2:c.1315A>T NP_001310602.1:p.Lys439Ter nonsense NM_001323674.2:c.1747A>T NP_001310603.1:p.Lys583Ter nonsense NM_001323675.2:c.1705A>T NP_001310604.1:p.Lys569Ter nonsense NM_001323676.2:c.1930A>T NP_001310605.1:p.Lys644Ter nonsense NM_001323677.2:c.1927A>T NP_001310606.1:p.Lys643Ter nonsense NM_001323678.2:c.1696A>T NP_001310607.1:p.Lys566Ter nonsense NM_030751.6:c.1969A>T NP_110378.3:p.Lys657Ter nonsense NR_024285.1:n.2682A>T NR_024286.1:n.2227A>T NR_024287.1:n.2564A>T NC_000010.11:g.31521304A>T NC_000010.10:g.31810232A>T NG_017048.1:g.207132A>T NG_017048.2:g.207889A>T - Protein change
- K439*, K583*, K590*, K643*, K566*, K637*, K644*, K657*, K658*, K569*, K640*, K641*
- Other names
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- Canonical SPDI
- NC_000010.11:31521303:A:T
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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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Apr 9, 2023 | RCV003688427.1 |
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
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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
(Apr 09, 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: SCV004455521.1
First in ClinVar: Feb 20, 2024 Last updated: Feb 20, 2024 |
Comment:
For these reasons, this variant has been classified as Pathogenic. This variant has not been reported in the literature in individuals affected with ZEB1-related conditions. … (more)
For these reasons, this variant has been classified as Pathogenic. This variant has not been reported in the literature in individuals affected with ZEB1-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change creates a premature translational stop signal (p.Lys657*) 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). (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 29, 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.