This variant is considered pathogenic. This variant creates a frameshift predicted to result in premature protein truncation.
ClinVar Genomic variation as it relates to human health
NM_001903.5(CTNNA1):c.1325_1328del (p.Asn442fs)
Germline
Classification
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criteria provided, single submitter. Learn more about how ClinVar calculates review status.
Pathogenic
This classification is based on the single submission received
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
Somatic
No data submitted for somatic clinical impact
Somatic
No data submitted for oncogenicity
Variant Details
- Identifiers
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NM_001903.5(CTNNA1):c.1325_1328del (p.Asn442fs)
Variation ID: 2673335 Accession: VCV002673335.1
- Type and length
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Deletion, 4 bp
- Location
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Cytogenetic: 5q31.2 5: 138904375-138904378 (GRCh38) [ NCBI UCSC ] 5: 138240064-138240067 (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 Dec 25, 2023 Dec 24, 2023 Sep 19, 2023 - HGVS
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... more HGVS ... less HGVSNucleotide Protein Molecular
consequenceNM_001903.5:c.1325_1328del MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_001894.2:p.Asn442fs frameshift NM_001290307.3:c.1325_1328del NP_001277236.1:p.Asn442fs frameshift NM_001290309.3:c.1016_1019del NP_001277238.1:p.Asn339fs frameshift NM_001290310.3:c.956_959del NP_001277239.1:p.Asn319fs frameshift NM_001290312.1:c.215_218del NP_001277241.1:p.Asn72fs frameshift NM_001323982.2:c.1325_1328del NP_001310911.1:p.Asn442fs frameshift NM_001323983.1:c.1325_1328del NP_001310912.1:p.Asn442fs frameshift NM_001323984.2:c.1325_1328del NP_001310913.1:p.Asn442fs frameshift NM_001323985.2:c.1325_1328del NP_001310914.1:p.Asn442fs frameshift NM_001323986.2:c.1297-13365_1297-13362del intron variant NM_001323987.1:c.215_218del NP_001310916.1:p.Asn72fs frameshift NM_001323988.1:c.215_218del NP_001310917.1:p.Asn72fs frameshift NM_001323989.1:c.215_218del NP_001310918.1:p.Asn72fs frameshift NM_001323990.1:c.215_218del NP_001310919.1:p.Asn72fs frameshift NM_001323991.1:c.215_218del NP_001310920.1:p.Asn72fs frameshift NM_001323992.1:c.215_218del NP_001310921.1:p.Asn72fs frameshift NM_001323993.1:c.215_218del NP_001310922.1:p.Asn72fs frameshift NM_001323994.1:c.215_218del NP_001310923.1:p.Asn72fs frameshift NM_001323995.1:c.215_218del NP_001310924.1:p.Asn72fs frameshift NM_001323996.1:c.215_218del NP_001310925.1:p.Asn72fs frameshift NM_001323997.1:c.215_218del NP_001310926.1:p.Asn72fs frameshift NM_001323998.1:c.215_218del NP_001310927.1:p.Asn72fs frameshift NM_001323999.1:c.215_218del NP_001310928.1:p.Asn72fs frameshift NM_001324000.1:c.215_218del NP_001310929.1:p.Asn72fs frameshift NM_001324001.1:c.215_218del NP_001310930.1:p.Asn72fs frameshift NM_001324002.1:c.215_218del NP_001310931.1:p.Asn72fs frameshift NM_001324003.1:c.215_218del NP_001310932.1:p.Asn72fs frameshift NM_001324004.1:c.215_218del NP_001310933.1:p.Asn72fs frameshift NM_001324005.1:c.215_218del NP_001310934.1:p.Asn72fs frameshift NM_001324006.1:c.-183_-180del 5 prime UTR NM_001324007.1:c.-183_-180del 5 prime UTR NM_001324008.1:c.-183_-180del 5 prime UTR NM_001324009.1:c.-183_-180del 5 prime UTR NM_001324010.1:c.-60-13365_-60-13362del intron variant NM_001324011.1:c.187-13365_187-13362del intron variant NM_001324012.1:c.-29_-26del 5 prime UTR NM_001324013.1:c.-29_-26del 5 prime UTR NC_000005.10:g.138904377_138904380del NC_000005.9:g.138240066_138240069del NG_047029.1:g.155982_155985del - Protein change
- N319fs, N339fs, N442fs, N72fs
- Other names
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- Canonical SPDI
- NC_000005.10:138904374:AAATAA:AA
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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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| CTNNA1 | Sufficient evidence for dosage pathogenicity | No evidence available |
GRCh38 GRCh37 |
3141 | 3205 | |
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. |
|---|---|---|---|---|
| Pathogenic (1) |
criteria provided, single submitter
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Sep 19, 2023 | RCV003455960.1 |
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
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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
(Sep 19, 2023)
C
Contributing to aggregate classification
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criteria provided, single submitter
Method: clinical testing
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Hereditary diffuse gastric adenocarcinoma
Affected status: unknown
Allele origin:
unknown
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Myriad Genetics, Inc.
Accession: SCV004186900.1
First in ClinVar: Dec 24, 2023 Last updated: Dec 24, 2023 |
Comment:
This variant is considered pathogenic. This variant creates a frameshift predicted to result in premature protein truncation.
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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:
This variant is considered pathogenic. This variant creates a frameshift predicted to result in premature protein truncation.
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 Dec 22, 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.