ClinVar Genomic variation as it relates to human health
NM_004329.3(BMPR1A):c.338del (p.Ser113fs)
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_004329.3(BMPR1A):c.338del (p.Ser113fs)
Variation ID: 2006853 Accession: VCV002006853.2
- Type and length
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Deletion, 1 bp
- Location
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Cytogenetic: 10q23.2 10: 86899798 (GRCh38) [ NCBI UCSC ] 10: 88659555 (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 Feb 8, 2023 Feb 20, 2024 Mar 21, 2023 - HGVS
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Nucleotide Protein Molecular
consequenceNM_004329.3:c.338del MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_004320.2:p.Ser113fs frameshift NM_001406559.1:c.338delC NP_001393488.1:p.Ser113Phefs frameshift NM_001406560.1:c.338delC NP_001393489.1:p.Ser113Phefs frameshift NM_001406561.1:c.338delC NP_001393490.1:p.Ser113Phefs frameshift NM_001406562.1:c.338delC NP_001393491.1:p.Ser113Phefs frameshift NM_001406563.1:c.338delC NP_001393492.1:p.Ser113Phefs frameshift NM_001406564.1:c.338delC NP_001393493.1:p.Ser113Phefs frameshift NM_001406565.1:c.338delC NP_001393494.1:p.Ser113Phefs frameshift NM_001406566.1:c.338delC NP_001393495.1:p.Ser113Phefs frameshift NM_001406567.1:c.338delC NP_001393496.1:p.Ser113Phefs frameshift NM_001406568.1:c.338delC NP_001393497.1:p.Ser113Phefs frameshift NM_001406569.1:c.338delC NP_001393498.1:p.Ser113Phefs frameshift NM_001406570.1:c.338delC NP_001393499.1:p.Ser113Phefs frameshift NM_001406571.1:c.338delC NP_001393500.1:p.Ser113Phefs frameshift NM_001406572.1:c.338delC NP_001393501.1:p.Ser113Phefs frameshift NM_001406573.1:c.338delC NP_001393502.1:p.Ser113Phefs frameshift NM_001406574.1:c.338delC NP_001393503.1:p.Ser113Phefs frameshift NM_001406575.1:c.338delC NP_001393504.1:p.Ser113Phefs frameshift NM_001406576.1:c.338delC NP_001393505.1:p.Ser113Phefs frameshift NM_001406577.1:c.338delC NP_001393506.1:p.Ser113Phefs frameshift NM_001406578.1:c.338delC NP_001393507.1:p.Ser113Phefs frameshift NM_001406579.1:c.338delC NP_001393508.1:p.Ser113Phefs frameshift NM_001406580.1:c.338delC NP_001393509.1:p.Ser113Phefs frameshift NM_001406581.1:c.338delC NP_001393510.1:p.Ser113Phefs frameshift NM_001406582.1:c.338delC NP_001393511.1:p.Ser113Phefs frameshift NM_001406583.1:c.338delC NP_001393512.1:p.Ser113Phefs frameshift NM_001406584.1:c.254delC NP_001393513.1:p.Ser85Phefs frameshift NM_001406585.1:c.254delC NP_001393514.1:p.Ser85Phefs frameshift NM_001406586.1:c.254delC NP_001393515.1:p.Ser85Phefs frameshift NM_001406587.1:c.254delC NP_001393516.1:p.Ser85Phefs frameshift NM_001406588.1:c.254delC NP_001393517.1:p.Ser85Phefs frameshift NR_176211.1:n.906delC NR_176212.1:n.906delC NR_176213.1:n.906delC NC_000010.11:g.86899798del NC_000010.10:g.88659555del NG_009362.1:g.148160del LRG_298:g.148160del LRG_298t1:c.338del LRG_298p1:p.Ser113Phefs - Protein change
- S113fs
- Other names
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- Canonical SPDI
- NC_000010.11:86899797: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
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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
Help
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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BMPR1A | Sufficient evidence for dosage pathogenicity | No evidence available |
GRCh38 GRCh37 |
2229 | 2323 |
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) |
criteria provided, single submitter
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Mar 21, 2023 | RCV002837950.2 |
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
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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
(Mar 21, 2023)
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criteria provided, single submitter
Method: clinical testing
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Juvenile polyposis syndrome
Affected status: unknown
Allele origin:
germline
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Invitae
Accession: SCV003208650.2
First in ClinVar: Feb 07, 2023 Last updated: Feb 20, 2024 |
Comment:
For these reasons, this variant has been classified as Pathogenic. ClinVar contains an entry for this variant (Variation ID: 2006853). This variant has not been … (more)
For these reasons, this variant has been classified as Pathogenic. ClinVar contains an entry for this variant (Variation ID: 2006853). This variant has not been reported in the literature in individuals affected with BMPR1A-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change creates a premature translational stop signal (p.Ser113Phefs*10) in the BMPR1A gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in BMPR1A are known to be pathogenic (PMID: 11536076, 12417513). (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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Germline SMAD4 or BMPR1A mutations and phenotype of juvenile polyposis. | Sayed MG | Annals of surgical oncology | 2002 | PMID: 12417513 |
Germline mutations in BMPR1A/ALK3 cause a subset of cases of juvenile polyposis syndrome and of Cowden and Bannayan-Riley-Ruvalcaba syndromes. | Zhou XP | American journal of human genetics | 2001 | PMID: 11536076 |
Text-mined citations for this variant ...
HelpRecord last updated Feb 29, 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.