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NC_000010.10:g.(?_88598623)_(88659889_?)del AND Juvenile polyposis syndrome

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Nov 16, 2019
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:
RCV001391045.2

Allele description [Variation Report for NC_000010.10:g.(?_88598623)_(88659889_?)del]

NC_000010.10:g.(?_88598623)_(88659889_?)del

Gene:
BMPR1A:bone morphogenetic protein receptor type 1A [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
10q23.2
Genomic location:
Chr10: 88598623 - 88659889 (on Assembly GRCh37)
Preferred name:
NC_000010.10:g.(?_88598623)_(88659889_?)del
HGVS:
NC_000010.10:g.(?_88598623)_(88659889_?)del

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
SCV001592983Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Pathogenic
(Nov 16, 2019) 		germlineclinical testing

PubMed (3)
[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

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

Germline SMAD4 or BMPR1A mutations and phenotype of juvenile polyposis.

Sayed MG, Ahmed AF, Ringold JR, Anderson ME, Bair JL, Mitros FA, Lynch HT, Tinley ST, Petersen GM, Giardiello FM, Vogelstein B, Howe JR.

Ann Surg Oncol. 2002 Nov;9(9):901-6.

PubMed [citation]
PMID:
12417513
See all PubMed Citations (3)

Details of each submission

From Invitae, SCV001592983.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (3)

Description

This variant is a gross deletion of the genomic region encompassing the promoter and coding exons 3-7 of the BMPR1A gene, which includes the initiator codon. The 5' end of this event is unknown as it extends beyond the assayed region for this gene and therefore may encompass additional genes. The 3' boundary is likely confined to intron 7 of the BMPR1A gene. This is expected to result in an absent or disrupted protein product. This variant has not been reported in the literature in individuals with BMPR1A-related conditions. Loss-of-function variants in BMPR1A are known to be pathogenic (PMID: 11536076, 12417513). For these reasons, this variant has been classified as Pathogenic.

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

Last Updated: Mar 26, 2023