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NM_004329.3(BMPR1A):c.1573_1588del (p.Met524_Val525insTer) AND Juvenile polyposis syndrome

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Nov 15, 2022
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:
RCV003762460.1

Allele description [Variation Report for NM_004329.3(BMPR1A):c.1573_1588del (p.Met524_Val525insTer)]

NM_004329.3(BMPR1A):c.1573_1588del (p.Met524_Val525insTer)

Gene:
BMPR1A:bone morphogenetic protein receptor type 1A [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
10q23.2
Genomic location:
Preferred name:
NM_004329.3(BMPR1A):c.1573_1588del (p.Met524_Val525insTer)
HGVS:
  • NC_000010.11:g.86923693_86923708del
  • NG_009362.1:g.172055_172070del
  • NM_001406559.1:c.1648_1663del
  • NM_001406560.1:c.1621_1636del
  • NM_001406561.1:c.1573_1588del
  • NM_001406562.1:c.1573_1588del
  • NM_001406563.1:c.1573_1588del
  • NM_001406564.1:c.1573_1588del
  • NM_001406565.1:c.1573_1588del
  • NM_001406566.1:c.1573_1588del
  • NM_001406567.1:c.1573_1588del
  • NM_001406568.1:c.1573_1588del
  • NM_001406569.1:c.1573_1588del
  • NM_001406570.1:c.1573_1588del
  • NM_001406571.1:c.1573_1588del
  • NM_001406572.1:c.1573_1588del
  • NM_001406573.1:c.1573_1588del
  • NM_001406574.1:c.1573_1588del
  • NM_001406575.1:c.1573_1588del
  • NM_001406576.1:c.1573_1588del
  • NM_001406577.1:c.1573_1588del
  • NM_001406578.1:c.1573_1588del
  • NM_001406579.1:c.1573_1588del
  • NM_001406580.1:c.1573_1588del
  • NM_001406581.1:c.1573_1588del
  • NM_001406582.1:c.1573_1588del
  • NM_001406583.1:c.1567_1582del
  • NM_001406584.1:c.1489_1504del
  • NM_001406585.1:c.1489_1504del
  • NM_001406586.1:c.1489_1504del
  • NM_001406587.1:c.1489_1504del
  • NM_001406588.1:c.1489_1504del
  • NM_001406589.1:c.1231_1246del
  • NM_004329.3:c.1573_1588delMANE SELECT
  • NP_001393488.1:p.Met549_Val550insTer
  • NP_001393489.1:p.Met540_Val541insTer
  • NP_001393490.1:p.Met524_Val525insTer
  • NP_001393491.1:p.Met524_Val525insTer
  • NP_001393492.1:p.Met524_Val525insTer
  • NP_001393493.1:p.Met524_Val525insTer
  • NP_001393494.1:p.Met524_Val525insTer
  • NP_001393495.1:p.Met524_Val525insTer
  • NP_001393496.1:p.Met524_Val525insTer
  • NP_001393497.1:p.Met524_Val525insTer
  • NP_001393498.1:p.Met524_Val525insTer
  • NP_001393499.1:p.Met524_Val525insTer
  • NP_001393500.1:p.Met524_Val525insTer
  • NP_001393501.1:p.Met524_Val525insTer
  • NP_001393502.1:p.Met524_Val525insTer
  • NP_001393503.1:p.Met524_Val525insTer
  • NP_001393504.1:p.Met524_Val525insTer
  • NP_001393505.1:p.Met524_Val525insTer
  • NP_001393506.1:p.Met524_Val525insTer
  • NP_001393507.1:p.Met524_Val525insTer
  • NP_001393508.1:p.Met524_Val525insTer
  • NP_001393509.1:p.Met524_Val525insTer
  • NP_001393510.1:p.Met524_Val525insTer
  • NP_001393511.1:p.Met524_Val525insTer
  • NP_001393512.1:p.Met522_Val523insTer
  • NP_001393513.1:p.Met496_Val497insTer
  • NP_001393514.1:p.Met496_Val497insTer
  • NP_001393515.1:p.Met496_Val497insTer
  • NP_001393516.1:p.Met496_Val497insTer
  • NP_001393517.1:p.Met496_Val497insTer
  • NP_001393518.1:p.Met410_Val411insTer
  • NP_004320.2:p.Met524_Val525insTer
  • NP_004320.2:p.Val525Terfs
  • LRG_298t1:c.1573_1588del16
  • LRG_298:g.172055_172070del
  • LRG_298p1:p.Val525Terfs
  • NC_000010.10:g.88683442_88683457del
  • NC_000010.10:g.88683450_88683465del
  • NM_004329.2:c.1573_1588del16
  • NR_176211.1:n.2141_2156del
  • NR_176212.1:n.2141_2156del
  • NR_176213.1:n.2141_2156del
Molecular consequence:
  • NR_176211.1:n.2141_2156del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_176212.1:n.2141_2156del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_176213.1:n.2141_2156del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NM_001406559.1:c.1648_1663del - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001406560.1:c.1621_1636del - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001406561.1:c.1573_1588del - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001406562.1:c.1573_1588del - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001406563.1:c.1573_1588del - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001406564.1:c.1573_1588del - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001406565.1:c.1573_1588del - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001406566.1:c.1573_1588del - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001406567.1:c.1573_1588del - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001406568.1:c.1573_1588del - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001406569.1:c.1573_1588del - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001406570.1:c.1573_1588del - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001406571.1:c.1573_1588del - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001406572.1:c.1573_1588del - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001406573.1:c.1573_1588del - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001406574.1:c.1573_1588del - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001406575.1:c.1573_1588del - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001406576.1:c.1573_1588del - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001406577.1:c.1573_1588del - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001406578.1:c.1573_1588del - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001406579.1:c.1573_1588del - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001406580.1:c.1573_1588del - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001406581.1:c.1573_1588del - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001406582.1:c.1573_1588del - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001406583.1:c.1567_1582del - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001406584.1:c.1489_1504del - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001406585.1:c.1489_1504del - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001406586.1:c.1489_1504del - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001406587.1:c.1489_1504del - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001406588.1:c.1489_1504del - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001406589.1:c.1231_1246del - nonsense - [Sequence Ontology: SO:0001587]
  • NM_004329.3:c.1573_1588del - nonsense - [Sequence Ontology: SO:0001587]

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
SCV004409240Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(Nov 15, 2022) 		germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

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

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240-242.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From Invitae, SCV004409240.1

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

Description

This variant is not present in population databases (gnomAD no frequency). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. This variant has not been reported in the literature in individuals affected with BMPR1A-related conditions. This sequence change creates a premature translational stop signal (p.Val525*) in the BMPR1A gene. While this is not anticipated to result in nonsense mediated decay, it is expected to disrupt the last 8 amino acid(s) of the BMPR1A protein.

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

Last Updated: Feb 28, 2024