ClinVar Genomic variation as it relates to human health
NM_001174096.2(ZEB1):c.2919_2920del (p.Gly974fs)
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.2919_2920del (p.Gly974fs)
Variation ID: 12631 Accession: VCV000012631.2
- Type and length
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Deletion, 2 bp
- Location
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Cytogenetic: 10p11.22 10: 31526805-31526806 (GRCh38) [ NCBI UCSC ] 10: 31815733-31815734 (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 Jan 21, 2018 Mar 18, 2023 Nov 1, 2005 - HGVS
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Nucleotide Protein Molecular
consequenceNM_001174096.2:c.2919_2920del MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_001167567.1:p.Gly974fs frameshift NM_001128128.3:c.2868_2869del NP_001121600.1:p.Gly957fs frameshift NM_001174093.2:c.2856_2857del NP_001167564.1:p.Gly953fs frameshift NM_001174094.2:c.2865_2866del NP_001167565.1:p.Gly956fs frameshift NM_001174095.2:c.2715_2716del NP_001167566.1:p.Gly906fs frameshift NM_001323638.2:c.2262_2263del NP_001310567.1:p.Gly755fs frameshift NM_001323641.2:c.2262_2263del NP_001310570.1:p.Gly755fs frameshift NM_001323642.2:c.2262_2263del NP_001310571.1:p.Gly755fs frameshift NM_001323643.2:c.2262_2263del NP_001310572.1:p.Gly755fs frameshift NM_001323644.2:c.2262_2263del NP_001310573.1:p.Gly755fs frameshift NM_001323645.2:c.2262_2263del NP_001310574.1:p.Gly755fs frameshift NM_001323646.2:c.2262_2263del NP_001310575.1:p.Gly755fs frameshift NM_001323647.2:c.2262_2263del NP_001310576.1:p.Gly755fs frameshift NM_001323648.2:c.2262_2263del NP_001310577.1:p.Gly755fs frameshift NM_001323649.2:c.2262_2263del NP_001310578.1:p.Gly755fs frameshift NM_001323650.2:c.2262_2263del NP_001310579.1:p.Gly755fs frameshift NM_001323651.2:c.2262_2263del NP_001310580.1:p.Gly755fs frameshift NM_001323652.2:c.2262_2263del NP_001310581.1:p.Gly755fs frameshift NM_001323653.2:c.2262_2263del NP_001310582.1:p.Gly755fs frameshift NM_001323654.2:c.2262_2263del NP_001310583.1:p.Gly755fs frameshift NM_001323655.2:c.2262_2263del NP_001310584.1:p.Gly755fs frameshift NM_001323656.2:c.2262_2263del NP_001310585.1:p.Gly755fs frameshift NM_001323657.2:c.2262_2263del NP_001310586.1:p.Gly755fs frameshift NM_001323658.2:c.2262_2263del NP_001310587.1:p.Gly755fs frameshift NM_001323659.2:c.2262_2263del NP_001310588.1:p.Gly755fs frameshift NM_001323660.2:c.2262_2263del NP_001310589.1:p.Gly755fs frameshift NM_001323661.2:c.2262_2263del NP_001310590.1:p.Gly755fs frameshift NM_001323662.2:c.2262_2263del NP_001310591.1:p.Gly755fs frameshift NM_001323663.2:c.2262_2263del NP_001310592.1:p.Gly755fs frameshift NM_001323664.2:c.2262_2263del NP_001310593.1:p.Gly755fs frameshift NM_001323665.2:c.2262_2263del NP_001310594.1:p.Gly755fs frameshift NM_001323666.2:c.2262_2263del NP_001310595.1:p.Gly755fs frameshift NM_001323671.2:c.2262_2263del NP_001310600.1:p.Gly755fs frameshift NM_001323672.2:c.2262_2263del NP_001310601.1:p.Gly755fs frameshift NM_001323673.2:c.2262_2263del NP_001310602.1:p.Gly755fs frameshift NM_001323674.2:c.2694_2695del NP_001310603.1:p.Gly899fs frameshift NM_001323675.2:c.2652_2653del NP_001310604.1:p.Gly885fs frameshift NM_001323676.2:c.2877_2878del NP_001310605.1:p.Gly960fs frameshift NM_001323677.2:c.2874_2875del NP_001310606.1:p.Gly959fs frameshift NM_001323678.2:c.2643_2644del NP_001310607.1:p.Gly882fs frameshift NM_030751.6:c.2916_2917del NP_110378.3:p.Gly973fs frameshift NC_000010.11:g.31526805_31526806del NC_000010.10:g.31815733_31815734del NG_017048.1:g.212633_212634del - Protein change
- G906fs, G882fs, G885fs, G960fs, G974fs, G755fs, G953fs, G959fs, G973fs, G899fs, G956fs, G957fs
- Other names
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- Canonical SPDI
- NC_000010.11:31526804:TG:
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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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- Comment on variant
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
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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Pathogenic (1) |
no assertion criteria provided
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Nov 1, 2005 | RCV000013466.26 |
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
(Nov 01, 2005)
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no assertion criteria provided
Method: literature only
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CORNEAL DYSTROPHY, POSTERIOR POLYMORPHOUS, 3
Affected status: not provided
Allele origin:
germline
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OMIM
Accession: SCV000033713.3
First in ClinVar: Apr 04, 2013 Last updated: Mar 18, 2023 |
Comment on evidence:
In the original family (UM:139) with posterior polymorphous corneal dystrophy-3 (PPCD3; 609141) described by Moroi et al. (2003), Krafchak et al. (2005) detected a heterozygous … (more)
In the original family (UM:139) with posterior polymorphous corneal dystrophy-3 (PPCD3; 609141) described by Moroi et al. (2003), Krafchak et al. (2005) detected a heterozygous 2-bp deletion in the last exon of the TCF8 gene, c.2916_2917delTG (c.2916_2917delTG, NM_030751). This frameshift mutation was predicted to alter the amino acids downstream of the deletion and maintain an open reading frame for 13 codons before a termination signal, resulting in elimination of most of the last zinc finger cluster and the acidic activation domain. The mutation was present in all 13 affected family members who were screened. (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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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 |
Clinicopathologic correlation and genetic analysis in a case of posterior polymorphous corneal dystrophy. | Moroi SE | American journal of ophthalmology | 2003 | PMID: 12654361 |
Text-mined citations for rs1592143384 ...
HelpRecord last updated Mar 18, 2023
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.
ClinGen staff contributed the HGVS expression for this variant.