ClinVar Genomic variation as it relates to human health
NM_001174096.2(ZEB1):c.998T>C (p.Ile333Thr)
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.998T>C (p.Ile333Thr)
Variation ID: 1298478 Accession: VCV001298478.16
- Type and length
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single nucleotide variant, 1 bp
- Location
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Cytogenetic: 10p11.22 10: 31520330 (GRCh38) [ NCBI UCSC ] 10: 31809258 (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 Oct 8, 2021 Apr 15, 2024 Aug 30, 2023 - HGVS
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Nucleotide Protein Molecular
consequenceNM_001174096.2:c.998T>C MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_001167567.1:p.Ile333Thr missense NM_001128128.3:c.947T>C NP_001121600.1:p.Ile316Thr missense NM_001174093.2:c.935T>C NP_001167564.1:p.Ile312Thr missense NM_001174094.2:c.944T>C NP_001167565.1:p.Ile315Thr missense NM_001174095.2:c.794T>C NP_001167566.1:p.Ile265Thr missense NM_001323638.2:c.341T>C NP_001310567.1:p.Ile114Thr missense NM_001323641.2:c.341T>C NP_001310570.1:p.Ile114Thr missense NM_001323642.2:c.341T>C NP_001310571.1:p.Ile114Thr missense NM_001323643.2:c.341T>C NP_001310572.1:p.Ile114Thr missense NM_001323644.2:c.341T>C NP_001310573.1:p.Ile114Thr missense NM_001323645.2:c.341T>C NP_001310574.1:p.Ile114Thr missense NM_001323646.2:c.341T>C NP_001310575.1:p.Ile114Thr missense NM_001323647.2:c.341T>C NP_001310576.1:p.Ile114Thr missense NM_001323648.2:c.341T>C NP_001310577.1:p.Ile114Thr missense NM_001323649.2:c.341T>C NP_001310578.1:p.Ile114Thr missense NM_001323650.2:c.341T>C NP_001310579.1:p.Ile114Thr missense NM_001323651.2:c.341T>C NP_001310580.1:p.Ile114Thr missense NM_001323652.2:c.341T>C NP_001310581.1:p.Ile114Thr missense NM_001323653.2:c.341T>C NP_001310582.1:p.Ile114Thr missense NM_001323654.2:c.341T>C NP_001310583.1:p.Ile114Thr missense NM_001323655.2:c.341T>C NP_001310584.1:p.Ile114Thr missense NM_001323656.2:c.341T>C NP_001310585.1:p.Ile114Thr missense NM_001323657.2:c.341T>C NP_001310586.1:p.Ile114Thr missense NM_001323658.2:c.341T>C NP_001310587.1:p.Ile114Thr missense NM_001323659.2:c.341T>C NP_001310588.1:p.Ile114Thr missense NM_001323660.2:c.341T>C NP_001310589.1:p.Ile114Thr missense NM_001323661.2:c.341T>C NP_001310590.1:p.Ile114Thr missense NM_001323662.2:c.341T>C NP_001310591.1:p.Ile114Thr missense NM_001323663.2:c.341T>C NP_001310592.1:p.Ile114Thr missense NM_001323664.2:c.341T>C NP_001310593.1:p.Ile114Thr missense NM_001323665.2:c.341T>C NP_001310594.1:p.Ile114Thr missense NM_001323666.2:c.341T>C NP_001310595.1:p.Ile114Thr missense NM_001323671.2:c.341T>C NP_001310600.1:p.Ile114Thr missense NM_001323672.2:c.341T>C NP_001310601.1:p.Ile114Thr missense NM_001323673.2:c.341T>C NP_001310602.1:p.Ile114Thr missense NM_001323674.2:c.773T>C NP_001310603.1:p.Ile258Thr missense NM_001323675.2:c.731T>C NP_001310604.1:p.Ile244Thr missense NM_001323676.2:c.956T>C NP_001310605.1:p.Ile319Thr missense NM_001323677.2:c.953T>C NP_001310606.1:p.Ile318Thr missense NM_001323678.2:c.722T>C NP_001310607.1:p.Ile241Thr missense NM_030751.6:c.995T>C NP_110378.3:p.Ile332Thr missense NC_000010.11:g.31520330T>C NC_000010.10:g.31809258T>C NG_017048.1:g.206158T>C - Protein change
- I114T, I241T, I244T, I258T, I265T, I312T, I315T, I316T, I318T, I319T, I332T, I333T
- Other names
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- Canonical SPDI
- NC_000010.11:31520329:T:C
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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
Help
The frequency of the allele represented by this VCV record.
Exome Aggregation Consortium (ExAC) 0.00002
Trans-Omics for Precision Medicine (TOPMed) 0.00003
The Genome Aggregation Database (gnomAD) 0.00004
The Genome Aggregation Database (gnomAD), exomes 0.00004
- 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 | ||
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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 |
101 | 119 |
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
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
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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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Uncertain significance (2) |
criteria provided, multiple submitters, no conflicts
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Aug 30, 2023 | RCV001726808.15 |
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
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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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Uncertain significance
(Aug 30, 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: SCV004682463.1
First in ClinVar: Feb 28, 2024 Last updated: Feb 28, 2024 |
Comment:
In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant … (more)
In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt ZEB1 protein function. ClinVar contains an entry for this variant (Variation ID: 1298478). This sequence change replaces isoleucine, which is neutral and non-polar, with threonine, which is neutral and polar, at codon 332 of the ZEB1 protein (p.Ile332Thr). This variant is present in population databases (rs747652843, gnomAD 0.01%). This variant has not been reported in the literature in individuals affected with ZEB1-related conditions. (less)
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Uncertain significance
(Mar 01, 2022)
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criteria provided, single submitter
Method: clinical testing
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not provided
Affected status: yes
Allele origin:
germline
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CeGaT Center for Human Genetics Tuebingen
Accession: SCV001961202.14
First in ClinVar: Oct 08, 2021 Last updated: Apr 15, 2024 |
Number of individuals with the variant: 2
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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
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 rs747652843 ...
HelpRecord last updated Apr 15, 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.