The variant is not observed in the gnomAD v2.1.1 dataset. This variant was predicted to result in a loss or disruption of normal protein function through nonsense-mediated decay (NMD) or protein truncation. Multiple pathogenic variants are reported downstream of the variant. Therefore, this variant is classified as Likely pathogenic according to the recommendation of ACMG/AMP guideline.
ClinVar Genomic variation as it relates to human health
NM_001174096.2(ZEB1):c.831del (p.Ser279fs)
Germline
Classification
Help
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.
(1)
Help
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.
Likely pathogenic
1
criteria provided, single submitter
Somatic
No data submitted for somatic clinical impact
Somatic
No data submitted for oncogenicity
Variant Details
- Identifiers
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NM_001174096.2(ZEB1):c.831del (p.Ser279fs)
Variation ID: 2444117 Accession: VCV002444117.1
- Type and length
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Deletion, 1 bp
- Location
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Cytogenetic: 10p11.22 10: 31520163 (GRCh38) [ NCBI UCSC ] 10: 31809091 (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 Mar 18, 2023 Mar 18, 2023 Feb 23, 2023 - HGVS
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... more HGVS ... less HGVSNucleotide Protein Molecular
consequenceNM_001174096.2:c.831del MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_001167567.1:p.Ser279fs frameshift NM_001128128.3:c.780del NP_001121600.1:p.Ser262fs frameshift NM_001174093.2:c.768del NP_001167564.1:p.Ser258fs frameshift NM_001174094.2:c.777del NP_001167565.1:p.Ser261fs frameshift NM_001174095.2:c.627del NP_001167566.1:p.Ser211fs frameshift NM_001323638.2:c.174del NP_001310567.1:p.Ser60fs frameshift NM_001323641.2:c.174del NP_001310570.1:p.Ser60fs frameshift NM_001323642.2:c.174del NP_001310571.1:p.Ser60fs frameshift NM_001323643.2:c.174del NP_001310572.1:p.Ser60fs frameshift NM_001323644.2:c.174del NP_001310573.1:p.Ser60fs frameshift NM_001323645.2:c.174del NP_001310574.1:p.Ser60fs frameshift NM_001323646.2:c.174del NP_001310575.1:p.Ser60fs frameshift NM_001323647.2:c.174del NP_001310576.1:p.Ser60fs frameshift NM_001323648.2:c.174del NP_001310577.1:p.Ser60fs frameshift NM_001323649.2:c.174del NP_001310578.1:p.Ser60fs frameshift NM_001323650.2:c.174del NP_001310579.1:p.Ser60fs frameshift NM_001323651.2:c.174del NP_001310580.1:p.Ser60fs frameshift NM_001323652.2:c.174del NP_001310581.1:p.Ser60fs frameshift NM_001323653.2:c.174del NP_001310582.1:p.Ser60fs frameshift NM_001323654.2:c.174del NP_001310583.1:p.Ser60fs frameshift NM_001323655.2:c.174del NP_001310584.1:p.Ser60fs frameshift NM_001323656.2:c.174del NP_001310585.1:p.Ser60fs frameshift NM_001323657.2:c.174del NP_001310586.1:p.Ser60fs frameshift NM_001323658.2:c.174del NP_001310587.1:p.Ser60fs frameshift NM_001323659.2:c.174del NP_001310588.1:p.Ser60fs frameshift NM_001323660.2:c.174del NP_001310589.1:p.Ser60fs frameshift NM_001323661.2:c.174del NP_001310590.1:p.Ser60fs frameshift NM_001323662.2:c.174del NP_001310591.1:p.Ser60fs frameshift NM_001323663.2:c.174del NP_001310592.1:p.Ser60fs frameshift NM_001323664.2:c.174del NP_001310593.1:p.Ser60fs frameshift NM_001323665.2:c.174del NP_001310594.1:p.Ser60fs frameshift NM_001323666.2:c.174del NP_001310595.1:p.Ser60fs frameshift NM_001323671.2:c.174del NP_001310600.1:p.Ser60fs frameshift NM_001323672.2:c.174del NP_001310601.1:p.Ser60fs frameshift NM_001323673.2:c.174del NP_001310602.1:p.Ser60fs frameshift NM_001323674.2:c.606del NP_001310603.1:p.Ser204fs frameshift NM_001323675.2:c.564del NP_001310604.1:p.Ser190fs frameshift NM_001323676.2:c.789del NP_001310605.1:p.Ser265fs frameshift NM_001323677.2:c.786del NP_001310606.1:p.Ser264fs frameshift NM_001323678.2:c.555del NP_001310607.1:p.Ser187fs frameshift NM_030751.6:c.828del NP_110378.3:p.Ser278fs frameshift NR_024285.1:n.1541delC NR_024286.1:n.1086delC NR_024287.1:n.1423delC NC_000010.11:g.31520163del NC_000010.10:g.31809091del NG_017048.1:g.205991del NG_017048.2:g.206748del - Protein change
- S187fs, S190fs, S204fs, S211fs, S258fs, S261fs, S262fs, S264fs, S265fs, S278fs, S279fs, S60fs
- Other names
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- Canonical SPDI
- NC_000010.11:31520162: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.
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- 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. |
|||
| ZEB1 | - | - |
GRCh38 GRCh37 |
129 | 147 | |
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. |
|---|---|---|---|---|
| Likely pathogenic (1) |
criteria provided, single submitter
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Feb 23, 2023 | RCV003152915.1 |
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. |
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|---|---|---|---|---|---|
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Likely pathogenic
(Feb 23, 2023)
|
criteria provided, single submitter
Method: clinical testing
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Corneal dystrophy, Fuchs endothelial, 6
Affected status: yes
Allele origin:
unknown
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3billion
Accession: SCV003841449.1
First in ClinVar: Mar 18, 2023 Last updated: Mar 18, 2023 |
Comment:
The variant is not observed in the gnomAD v2.1.1 dataset. This variant was predicted to result in a loss or disruption of normal protein function … (more)
The variant is not observed in the gnomAD v2.1.1 dataset. This variant was predicted to result in a loss or disruption of normal protein function through nonsense-mediated decay (NMD) or protein truncation. Multiple pathogenic variants are reported downstream of the variant. Therefore, this variant is classified as Likely pathogenic according to the recommendation of ACMG/AMP guideline. (less)
Clinical Features:
Corneal opacity (present) , Hypopigmentation of the skin (present)
|
Comment:
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. |
Comment:
The variant is not observed in the gnomAD v2.1.1 dataset. This variant was predicted to result in a loss or disruption of normal protein function through nonsense-mediated decay (NMD) or protein truncation. Multiple pathogenic variants are reported downstream of the variant. Therefore, this variant is classified as Likely pathogenic according to the recommendation of ACMG/AMP guideline.
Citations for germline classification of this variant
Help| There 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 Mar 26, 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.