The c.2331delT (p.G779Vfs*2) alteration, located in exon 13 (coding exon 13) of the ATP2B1 gene, consists of a deletion of one nucleotide at position 2331, causing a translational frameshift with a predicted alternate stop codon after 2 amino acids. This alteration is expected to result in premature protein truncation or nonsense-mediated mRNA decay. However, loss of function of ATP2B1 has not been established as a mechanism of disease. Based on data from gnomAD, this allele has an overall frequency of 0.001% (1/152236) total alleles studied. The highest observed frequency was 0.0024% (1/41460) of African/African American alleles. Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.
ClinVar Genomic variation as it relates to human health
NM_001366521.1(ATP2B1):c.2331del (p.Gly779fs)
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)
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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.
Uncertain significance
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_001366521.1(ATP2B1):c.2331del (p.Gly779fs)
Variation ID: 2601163 Accession: VCV002601163.2
- Type and length
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Deletion, 1 bp
- Location
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Cytogenetic: 12q21.33 12: 89610425 (GRCh38) [ NCBI UCSC ] 12: 90004202 (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 28, 2023 May 1, 2024 Jul 25, 2023 - HGVS
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... more HGVS ... less HGVSNucleotide Protein Molecular
consequenceNM_001366521.1:c.2331del MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_001353450.1:p.Gly779fs frameshift NM_001001323.2:c.2331del NP_001001323.1:p.Gly779fs frameshift NM_001366520.1:c.2331del NP_001353449.1:p.Gly779fs frameshift NM_001366522.1:c.2331del NP_001353451.1:p.Gly779fs frameshift NM_001366523.1:c.2331del NP_001353452.1:p.Gly779fs frameshift NM_001366524.1:c.2331del NP_001353453.1:p.Gly779fs frameshift NM_001366525.1:c.2331del NP_001353454.1:p.Gly779fs frameshift NM_001366526.1:c.2331del NP_001353455.1:p.Gly779fs frameshift NM_001366527.1:c.2331del NP_001353456.1:p.Gly779fs frameshift NM_001366528.1:c.2331del NP_001353457.1:p.Gly779fs frameshift NM_001366529.1:c.2331del NP_001353458.1:p.Gly779fs frameshift NM_001366530.1:c.2133del NP_001353459.1:p.Gly713fs frameshift NM_001366531.1:c.1770del NP_001353460.1:p.Gly592fs frameshift NM_001366532.1:c.1770del NP_001353461.1:p.Gly592fs frameshift NM_001413046.1:c.2331del NP_001399975.1:p.Gly779fs frameshift NM_001413047.1:c.2331del NP_001399976.1:p.Gly779fs frameshift NM_001413048.1:c.2292del NP_001399977.1:p.Gly766fs frameshift NM_001413049.1:c.2331del NP_001399978.1:p.Gly779fs frameshift NM_001413050.1:c.2331del NP_001399979.1:p.Gly779fs frameshift NM_001413051.1:c.2190del NP_001399980.1:p.Gly732fs frameshift NM_001413052.1:c.2190del NP_001399981.1:p.Gly732fs frameshift NM_001413053.1:c.2133del NP_001399982.1:p.Gly713fs frameshift NM_001413054.1:c.2088del NP_001399983.1:p.Gly698fs frameshift NM_001413055.1:c.2190del NP_001399984.1:p.Gly732fs frameshift NM_001413056.1:c.2076del NP_001399985.1:p.Gly694fs frameshift NM_001413057.1:c.1878del NP_001399986.1:p.Gly628fs frameshift NM_001413058.1:c.1770del NP_001399987.1:p.Gly592fs frameshift NM_001413059.1:c.1770del NP_001399988.1:p.Gly592fs frameshift NM_001413060.1:c.1770del NP_001399989.1:p.Gly592fs frameshift NM_001682.3:c.2331del NP_001673.2:p.Gly779fs frameshift NR_182093.1:n.2700del non-coding transcript variant NR_182094.1:n.2700del non-coding transcript variant NR_182095.1:n.2795del non-coding transcript variant NC_000012.12:g.89610426del NC_000012.11:g.90004203del NG_029485.2:g.103929del - Protein change
- G628fs, G694fs, G779fs, G592fs, G732fs, G766fs, G713fs, G698fs
- Other names
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- Canonical SPDI
- NC_000012.12:89610424:AA:A
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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. |
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| ATP2B1 | - | - |
GRCh38 GRCh37 |
120 | 131 | |
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. |
|---|---|---|---|---|
| Uncertain significance (1) |
criteria provided, single submitter
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Jul 25, 2023 | RCV003359282.2 |
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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Uncertain significance
(Jul 25, 2023)
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criteria provided, single submitter
Method: clinical testing
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Inborn genetic diseases
Affected status: unknown
Allele origin:
germline
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Ambry Genetics
Accession: SCV004069783.2
First in ClinVar: Oct 28, 2023 Last updated: May 01, 2024 |
Comment:
The c.2331delT (p.G779Vfs*2) alteration, located in exon 13 (coding exon 13) of the ATP2B1 gene, consists of a deletion of one nucleotide at position 2331, … (more)
The c.2331delT (p.G779Vfs*2) alteration, located in exon 13 (coding exon 13) of the ATP2B1 gene, consists of a deletion of one nucleotide at position 2331, causing a translational frameshift with a predicted alternate stop codon after 2 amino acids. This alteration is expected to result in premature protein truncation or nonsense-mediated mRNA decay. However, loss of function of ATP2B1 has not been established as a mechanism of disease. Based on data from gnomAD, this allele has an overall frequency of 0.001% (1/152236) total alleles studied. The highest observed frequency was 0.0024% (1/41460) of African/African American alleles. Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. (less)
|
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 c.2331delT (p.G779Vfs*2) alteration, located in exon 13 (coding exon 13) of the ATP2B1 gene, consists of a deletion of one nucleotide at position 2331, causing a translational frameshift with a predicted alternate stop codon after 2 amino acids. This alteration is expected to result in premature protein truncation or nonsense-mediated mRNA decay. However, loss of function of ATP2B1 has not been established as a mechanism of disease. Based on data from gnomAD, this allele has an overall frequency of 0.001% (1/152236) total alleles studied. The highest observed frequency was 0.0024% (1/41460) of African/African American alleles. Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.
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 May 01, 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.