The frameshift c.916delp.Tyr306IlefsTer2 variant has not been reported previously as a pathogenic variant nor as a benign variant, to our knowledge. The p.Tyr306IlefsTer2 variant is novel not in any individuals in gnomAD Exomes and 1000 Genomes. This variant has not been reported to the ClinVar database. This variant causes a frameshift starting with codon Tyrosine 306, changes this amino acid to Isoleucine residue, and creates a premature Stop codon at position 2 of the new reading frame, denoted p.Tyr306IlefsTer2. This variant is predicted to cause loss of normal protein function through protein truncation. Loss of function variants have been previously reported to be disease causing. For these reasons, this variant has been classified as Likely Pathogenic.
ClinVar Genomic variation as it relates to human health
NM_004329.3(BMPR1A):c.916del (p.Tyr306fs)
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)
Help
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.
Likely pathogenic
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_004329.3(BMPR1A):c.916del (p.Tyr306fs)
Variation ID: 3236417 Accession: VCV003236417.2
- Type and length
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Deletion, 1 bp
- Location
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Cytogenetic: 10q23.2 10: 86919219 (GRCh38) [ NCBI UCSC ] 10: 88678976 (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 May 27, 2024 Jun 17, 2024 - HGVS
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... more HGVS ... less HGVSNucleotide Protein Molecular
consequenceNM_004329.3:c.916del MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_004320.2:p.Tyr306fs frameshift NM_001406559.1:c.991del NP_001393488.1:p.Tyr331fs frameshift NM_001406560.1:c.964del NP_001393489.1:p.Tyr322fs frameshift NM_001406561.1:c.916del NP_001393490.1:p.Tyr306fs frameshift NM_001406562.1:c.916del NP_001393491.1:p.Tyr306fs frameshift NM_001406563.1:c.916del NP_001393492.1:p.Tyr306fs frameshift NM_001406564.1:c.916del NP_001393493.1:p.Tyr306fs frameshift NM_001406565.1:c.916del NP_001393494.1:p.Tyr306fs frameshift NM_001406566.1:c.916del NP_001393495.1:p.Tyr306fs frameshift NM_001406567.1:c.916del NP_001393496.1:p.Tyr306fs frameshift NM_001406568.1:c.916del NP_001393497.1:p.Tyr306fs frameshift NM_001406569.1:c.916del NP_001393498.1:p.Tyr306fs frameshift NM_001406570.1:c.916del NP_001393499.1:p.Tyr306fs frameshift NM_001406571.1:c.916del NP_001393500.1:p.Tyr306fs frameshift NM_001406572.1:c.916del NP_001393501.1:p.Tyr306fs frameshift NM_001406573.1:c.916del NP_001393502.1:p.Tyr306fs frameshift NM_001406574.1:c.916del NP_001393503.1:p.Tyr306fs frameshift NM_001406575.1:c.916del NP_001393504.1:p.Tyr306fs frameshift NM_001406576.1:c.916del NP_001393505.1:p.Tyr306fs frameshift NM_001406577.1:c.916del NP_001393506.1:p.Tyr306fs frameshift NM_001406578.1:c.916del NP_001393507.1:p.Tyr306fs frameshift NM_001406579.1:c.916del NP_001393508.1:p.Tyr306fs frameshift NM_001406580.1:c.916del NP_001393509.1:p.Tyr306fs frameshift NM_001406581.1:c.916del NP_001393510.1:p.Tyr306fs frameshift NM_001406582.1:c.916del NP_001393511.1:p.Tyr306fs frameshift NM_001406583.1:c.910del NP_001393512.1:p.Tyr304fs frameshift NM_001406584.1:c.832del NP_001393513.1:p.Tyr278fs frameshift NM_001406585.1:c.832del NP_001393514.1:p.Tyr278fs frameshift NM_001406586.1:c.832del NP_001393515.1:p.Tyr278fs frameshift NM_001406587.1:c.832del NP_001393516.1:p.Tyr278fs frameshift NM_001406588.1:c.832del NP_001393517.1:p.Tyr278fs frameshift NM_001406589.1:c.574del NP_001393518.1:p.Tyr192fs frameshift NR_176211.1:n.1484del non-coding transcript variant NR_176212.1:n.1484del non-coding transcript variant NR_176213.1:n.1484del non-coding transcript variant NC_000010.11:g.86919219del NC_000010.10:g.88678976del NG_009362.1:g.167581del LRG_298:g.167581del LRG_298t1:c.916del LRG_298p1:p.Tyr306Ilefs - Protein change
- Y192fs, Y278fs, Y304fs, Y306fs, Y322fs, Y331fs
- Other names
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- Canonical SPDI
- NC_000010.11:86919218:T:
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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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| BMPR1A | Sufficient evidence for dosage pathogenicity | No evidence available |
GRCh38 GRCh37 |
2441 | 2537 | |
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. |
|---|---|---|---|---|
| Likely pathogenic (1) |
criteria provided, single submitter
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- | RCV004555785.2 |
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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Likely pathogenic
(-)
|
criteria provided, single submitter
Method: clinical testing
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Juvenile polyposis syndrome
(Autosomal dominant inheritance)
Affected status: yes
Allele origin:
germline
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Neuberg Centre For Genomic Medicine, NCGM
Accession: SCV005044768.2
First in ClinVar: May 26, 2024 Last updated: Jun 17, 2024 |
Comment:
The frameshift c.916delp.Tyr306IlefsTer2 variant has not been reported previously as a pathogenic variant nor as a benign variant, to our knowledge. The p.Tyr306IlefsTer2 variant is … (more)
The frameshift c.916delp.Tyr306IlefsTer2 variant has not been reported previously as a pathogenic variant nor as a benign variant, to our knowledge. The p.Tyr306IlefsTer2 variant is novel not in any individuals in gnomAD Exomes and 1000 Genomes. This variant has not been reported to the ClinVar database. This variant causes a frameshift starting with codon Tyrosine 306, changes this amino acid to Isoleucine residue, and creates a premature Stop codon at position 2 of the new reading frame, denoted p.Tyr306IlefsTer2. This variant is predicted to cause loss of normal protein function through protein truncation. Loss of function variants have been previously reported to be disease causing. For these reasons, this variant has been classified as Likely Pathogenic. (less)
Clinical Features:
Neoplasm (present)
|
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 frameshift c.916delp.Tyr306IlefsTer2 variant has not been reported previously as a pathogenic variant nor as a benign variant, to our knowledge. The p.Tyr306IlefsTer2 variant is novel not in any individuals in gnomAD Exomes and 1000 Genomes. This variant has not been reported to the ClinVar database. This variant causes a frameshift starting with codon Tyrosine 306, changes this amino acid to Isoleucine residue, and creates a premature Stop codon at position 2 of the new reading frame, denoted p.Tyr306IlefsTer2. This variant is predicted to cause loss of normal protein function through protein truncation. Loss of function variants have been previously reported to be disease causing. For these reasons, this variant has been classified as Likely Pathogenic.
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 Jun 17, 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.