ClinVar Genomic variation as it relates to human health
NM_004329.3(BMPR1A):c.1171dup (p.Thr391fs)
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.1171dup (p.Thr391fs)
Variation ID: 2087232 Accession: VCV002087232.2
- Type and length
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Duplication, 1 bp
- Location
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Cytogenetic: 10q23.2 10: 86921523-86921524 (GRCh38) [ NCBI UCSC ] 10: 88681280-88681281 (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 Apr 5, 2022 - HGVS
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Nucleotide Protein Molecular
consequenceNM_004329.3:c.1171dup MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_004320.2:p.Thr391fs frameshift NM_001406559.1:c.1246dup NP_001393488.1:p.Thr416Asnfs frameshift NM_001406560.1:c.1219dup NP_001393489.1:p.Thr407Asnfs frameshift NM_001406561.1:c.1171dup NP_001393490.1:p.Thr391Asnfs frameshift NM_001406562.1:c.1171dup NP_001393491.1:p.Thr391Asnfs frameshift NM_001406563.1:c.1171dup NP_001393492.1:p.Thr391Asnfs frameshift NM_001406564.1:c.1171dup NP_001393493.1:p.Thr391Asnfs frameshift NM_001406565.1:c.1171dup NP_001393494.1:p.Thr391Asnfs frameshift NM_001406566.1:c.1171dup NP_001393495.1:p.Thr391Asnfs frameshift NM_001406567.1:c.1171dup NP_001393496.1:p.Thr391Asnfs frameshift NM_001406568.1:c.1171dup NP_001393497.1:p.Thr391Asnfs frameshift NM_001406569.1:c.1171dup NP_001393498.1:p.Thr391Asnfs frameshift NM_001406570.1:c.1171dup NP_001393499.1:p.Thr391Asnfs frameshift NM_001406571.1:c.1171dup NP_001393500.1:p.Thr391Asnfs frameshift NM_001406572.1:c.1171dup NP_001393501.1:p.Thr391Asnfs frameshift NM_001406573.1:c.1171dup NP_001393502.1:p.Thr391Asnfs frameshift NM_001406574.1:c.1171dup NP_001393503.1:p.Thr391Asnfs frameshift NM_001406575.1:c.1171dup NP_001393504.1:p.Thr391Asnfs frameshift NM_001406576.1:c.1171dup NP_001393505.1:p.Thr391Asnfs frameshift NM_001406577.1:c.1171dup NP_001393506.1:p.Thr391Asnfs frameshift NM_001406578.1:c.1171dup NP_001393507.1:p.Thr391Asnfs frameshift NM_001406579.1:c.1171dup NP_001393508.1:p.Thr391Asnfs frameshift NM_001406580.1:c.1171dup NP_001393509.1:p.Thr391Asnfs frameshift NM_001406581.1:c.1171dup NP_001393510.1:p.Thr391Asnfs frameshift NM_001406582.1:c.1171dup NP_001393511.1:p.Thr391Asnfs frameshift NM_001406583.1:c.1165dup NP_001393512.1:p.Thr389Asnfs frameshift NM_001406584.1:c.1087dup NP_001393513.1:p.Thr363Asnfs frameshift NM_001406585.1:c.1087dup NP_001393514.1:p.Thr363Asnfs frameshift NM_001406586.1:c.1087dup NP_001393515.1:p.Thr363Asnfs frameshift NM_001406587.1:c.1087dup NP_001393516.1:p.Thr363Asnfs frameshift NM_001406588.1:c.1087dup NP_001393517.1:p.Thr363Asnfs frameshift NM_001406589.1:c.829dup NP_001393518.1:p.Thr277Asnfs frameshift NR_176211.1:n.1739dup NR_176212.1:n.1739dup NR_176213.1:n.1739dup NC_000010.11:g.86921524dup NC_000010.10:g.88681281dup NG_009362.1:g.169886dup LRG_298:g.169886dup LRG_298t1:c.1171dup LRG_298p1:p.Thr391Asnfs - Protein change
- T391fs
- Other names
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- Canonical SPDI
- NC_000010.11:86921523:A: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
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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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BMPR1A | Sufficient evidence for dosage pathogenicity | No evidence available |
GRCh38 GRCh37 |
- | 2321 |
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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Apr 5, 2022 | RCV003009459.2 |
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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Pathogenic
(Apr 05, 2022)
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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: SCV003302651.2
First in ClinVar: Feb 07, 2023 Last updated: Feb 20, 2024 |
Comment:
For these reasons, this variant has been classified as Pathogenic. This variant has not been reported in the literature in individuals affected with BMPR1A-related conditions. … (more)
For these reasons, this variant has been classified as Pathogenic. 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.Thr391Asnfs*3) 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 20, 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.