ClinVar Genomic variation as it relates to human health
NM_130839.5(UBE3A):c.1820del (p.Gly607fs)
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_130839.5(UBE3A):c.1820del (p.Gly607fs)
Variation ID: 2444079 Accession: VCV002444079.1
- Type and length
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Deletion, 1 bp
- Location
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Cytogenetic: 15q11.2 15: 25356830 (GRCh38) [ NCBI UCSC ] 15: 25601977 (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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Nucleotide Protein Molecular
consequenceNM_130839.5:c.1820del MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_570854.1:p.Gly607fs frameshift NM_000462.5:c.1829del NP_000453.2:p.Gly610fs frameshift NM_001354505.1:c.1820del NP_001341434.1:p.Gly607fs frameshift NM_001354506.2:c.1760del NP_001341435.1:p.Gly587fs frameshift NM_001354507.2:c.1760del NP_001341436.1:p.Gly587fs frameshift NM_001354508.2:c.1760del NP_001341437.1:p.Gly587fs frameshift NM_001354509.2:c.1760del NP_001341438.1:p.Gly587fs frameshift NM_001354511.2:c.1760del NP_001341440.1:p.Gly587fs frameshift NM_001354512.2:c.1760del NP_001341441.1:p.Gly587fs frameshift NM_001354513.2:c.1760del NP_001341442.1:p.Gly587fs frameshift NM_001354523.2:c.1760del NP_001341452.1:p.Gly587fs frameshift NM_001354526.1:c.1760del NP_001341455.1:p.Gly587fs frameshift NM_001354538.2:c.1820del NP_001341467.1:p.Gly607fs frameshift NM_001354539.2:c.1760del NP_001341468.1:p.Gly587fs frameshift NM_001354540.2:c.1760del NP_001341469.1:p.Gly587fs frameshift NM_001354541.2:c.1760del NP_001341470.1:p.Gly587fs frameshift NM_001354542.2:c.1760del NP_001341471.1:p.Gly587fs frameshift NM_001354543.2:c.1760del NP_001341472.1:p.Gly587fs frameshift NM_001354544.2:c.1760del NP_001341473.1:p.Gly587fs frameshift NM_001354545.2:c.1820del NP_001341474.1:p.Gly607fs frameshift NM_001354546.2:c.1643del NP_001341475.1:p.Gly548fs frameshift NM_001354547.2:c.1760del NP_001341476.1:p.Gly587fs frameshift NM_001354548.2:c.1760del NP_001341477.1:p.Gly587fs frameshift NM_001354549.2:c.1760del NP_001341478.1:p.Gly587fs frameshift NM_001354550.2:c.569del NP_001341479.1:p.Gly190fs frameshift NM_001354551.2:c.509del NP_001341480.1:p.Gly170fs frameshift NM_001374461.1:c.1760del NP_001361390.1:p.Gly587fs frameshift NM_130838.4:c.1760del NP_570853.1:p.Gly587fs frameshift NR_148916.2:n.2332del non-coding transcript variant NC_000015.10:g.25356832del NC_000015.9:g.25601979del NG_009268.1:g.87152del LRG_15:g.87152del LRG_15t1:c.1758del LRG_15p1:p.Gly587Valfs - Protein change
- G170fs, G190fs, G548fs, G587fs, G607fs, G610fs
- Other names
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- Canonical SPDI
- NC_000015.10:25356829:CCC:CC
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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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UBE3A | Sufficient evidence for dosage pathogenicity | No evidence available |
GRCh38 GRCh37 |
34 | 1202 | |
SNHG14 | - | - | GRCh38 | 1 | 1101 |
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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Likely pathogenic (1) |
criteria provided, single submitter
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Feb 23, 2023 | RCV003152877.1 |
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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Likely pathogenic
(Feb 23, 2023)
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criteria provided, single submitter
Method: clinical testing
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Angelman syndrome
Affected status: yes
Allele origin:
unknown
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3billion
Accession: SCV003841366.1
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:
Neurodevelopmental delay (present) , Intellectual disability (present) , Abnormal facial shape (present) , Recurrent hand flapping (present)
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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 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.