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NM_004329.3(BMPR1A):c.333+2T>A AND Juvenile polyposis syndrome

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
Nov 12, 2021
Review status:
1 star out of maximum of 4 stars
criteria provided, single submitter
Somatic classification
of clinical impact:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Somatic classification
of oncogenicity:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Record status:
current
Accession:
RCV002015852.4

Allele description [Variation Report for NM_004329.3(BMPR1A):c.333+2T>A]

NM_004329.3(BMPR1A):c.333+2T>A

Gene:
BMPR1A:bone morphogenetic protein receptor type 1A [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
10q23.2
Genomic location:
Preferred name:
NM_004329.3(BMPR1A):c.333+2T>A
HGVS:
  • NC_000010.11:g.86892231T>A
  • NG_009362.1:g.140593T>A
  • NM_001406559.1:c.333+2T>A
  • NM_001406560.1:c.333+2T>A
  • NM_001406561.1:c.333+2T>A
  • NM_001406562.1:c.333+2T>A
  • NM_001406563.1:c.333+2T>A
  • NM_001406564.1:c.333+2T>A
  • NM_001406565.1:c.333+2T>A
  • NM_001406566.1:c.333+2T>A
  • NM_001406567.1:c.333+2T>A
  • NM_001406568.1:c.333+2T>A
  • NM_001406569.1:c.333+2T>A
  • NM_001406570.1:c.333+2T>A
  • NM_001406571.1:c.333+2T>A
  • NM_001406572.1:c.333+2T>A
  • NM_001406573.1:c.333+2T>A
  • NM_001406574.1:c.333+2T>A
  • NM_001406575.1:c.333+2T>A
  • NM_001406576.1:c.333+2T>A
  • NM_001406577.1:c.333+2T>A
  • NM_001406578.1:c.333+2T>A
  • NM_001406579.1:c.333+2T>A
  • NM_001406580.1:c.333+2T>A
  • NM_001406581.1:c.333+2T>A
  • NM_001406582.1:c.333+2T>A
  • NM_001406583.1:c.333+2T>A
  • NM_001406584.1:c.249+2T>A
  • NM_001406585.1:c.249+2T>A
  • NM_001406586.1:c.249+2T>A
  • NM_001406587.1:c.249+2T>A
  • NM_001406588.1:c.249+2T>A
  • NM_001406589.1:c.333+2T>A
  • NM_004329.3:c.333+2T>AMANE SELECT
  • LRG_298:g.140593T>A
  • NC_000010.10:g.88651988T>A
Links:
dbSNP: rs2133409163
NCBI 1000 Genomes Browser:
rs2133409163
Molecular consequence:
  • NM_001406559.1:c.333+2T>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406560.1:c.333+2T>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406561.1:c.333+2T>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406562.1:c.333+2T>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406563.1:c.333+2T>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406564.1:c.333+2T>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406565.1:c.333+2T>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406566.1:c.333+2T>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406567.1:c.333+2T>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406568.1:c.333+2T>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406569.1:c.333+2T>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406570.1:c.333+2T>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406571.1:c.333+2T>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406572.1:c.333+2T>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406573.1:c.333+2T>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406574.1:c.333+2T>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406575.1:c.333+2T>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406576.1:c.333+2T>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406577.1:c.333+2T>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406578.1:c.333+2T>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406579.1:c.333+2T>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406580.1:c.333+2T>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406581.1:c.333+2T>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406582.1:c.333+2T>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406583.1:c.333+2T>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406584.1:c.249+2T>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406585.1:c.249+2T>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406586.1:c.249+2T>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406587.1:c.249+2T>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406588.1:c.249+2T>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406589.1:c.333+2T>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_004329.3:c.333+2T>A - splice donor variant - [Sequence Ontology: SO:0001575]

Condition(s)

Name:
Juvenile polyposis syndrome (JPS)
Synonyms:
Polyposis juvenile intestinal; Polyposis familial of entire gastrointestinal tract
Identifiers:
MONDO: MONDO:0017380; MedGen: C0345893; Orphanet: 2929; OMIM: 174900

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002297138Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Likely pathogenic
(Nov 12, 2021) 		germlineclinical testing

PubMed (4)
[See all records that cite these PMIDs]

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Splicing in action: assessing disease causing sequence changes.

Baralle D, Baralle M.

J Med Genet. 2005 Oct;42(10):737-48. Review.

PubMed [citation]
PMID:
16199547
PMCID:
PMC1735933

Germline mutations in BMPR1A/ALK3 cause a subset of cases of juvenile polyposis syndrome and of Cowden and Bannayan-Riley-Ruvalcaba syndromes.

Zhou XP, Woodford-Richens K, Lehtonen R, Kurose K, Aldred M, Hampel H, Launonen V, Virta S, Pilarski R, Salovaara R, Bodmer WF, Conrad BA, Dunlop M, Hodgson SV, Iwama T, Järvinen H, Kellokumpu I, Kim JC, Leggett B, Markie D, Mecklin JP, Neale K, et al.

Am J Hum Genet. 2001 Oct;69(4):704-11. Epub 2001 Aug 30.

PubMed [citation]
PMID:
11536076
PMCID:
PMC1226057
See all PubMed Citations (4)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV002297138.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (4)

Description

In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. 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 affects a donor splice site in intron 5 of the BMPR1A gene. It is expected to disrupt RNA splicing. Variants that disrupt the donor or acceptor splice site typically lead to a loss of protein function (PMID: 16199547), and loss-of-function variants in BMPR1A are known to be pathogenic (PMID: 11536076, 12417513).

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Sep 29, 2024