NM_004329.3(BMPR1A):c.566dup (p.Tyr189Ter) AND Juvenile polyposis syndrome

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Aug 1, 2023
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:: RCV002233542.13

Allele description [Variation Report for NM_004329.3(BMPR1A):c.566dup (p.Tyr189Ter)]

NM_004329.3(BMPR1A):c.566dup (p.Tyr189Ter)

Gene:

BMPR1A:bone morphogenetic protein receptor type 1A [Gene - OMIM - HGNC]

Variant type:

Duplication

Cytogenetic location:

10q23.2

Genomic location:

Preferred name:

NM_004329.3(BMPR1A):c.566dup (p.Tyr189Ter)

HGVS:

NC_000010.11:g.86912275dup
NG_009362.1:g.160637dup
NM_004329.3:c.566dupMANE SELECT
NP_004320.2:p.Tyr189Ter
NP_004320.2:p.Tyr189Ter
LRG_298t1:c.566dup
LRG_298:g.160637dup
LRG_298p1:p.Tyr189Ter
NC_000010.10:g.88672031_88672032insA
NC_000010.10:g.88672032dup
NM_004329.2:c.566dup
NM_004329.2:c.566dupA

Protein change:

Y189*

Links:

dbSNP: rs1564721929

NCBI 1000 Genomes Browser:

rs1564721929

Molecular consequence:

NM_004329.3:c.566dup - 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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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000819998	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Aug 1, 2023)	germline	clinical testing	PubMed (4) [See all records that cite these PMIDs] 16152648, 11536076, 12417513, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000819998

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Aug 1, 2023)

germline

clinical testing

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

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Vessels' morphology in SMAD4 and BMPR1A-related juvenile polyposis.

Handra-Luca A, Condroyer C, de Moncuit C, Tepper M, Fléjou JF, Thomas G, Olschwang S.

Am J Med Genet A. 2005 Oct 1;138A(2):113-7.

PubMed [citation]

PMID:: 16152648

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 Invitae, SCV000819998.4

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (4)

Description

For these reasons, this variant has been classified as Pathogenic. ClinVar contains an entry for this variant (Variation ID: 571137). This premature translational stop signal has been observed in individual(s) with juvenile polyposis syndrome (PMID: 16152648). This variant is not present in population databases (gnomAD no frequency). This sequence change creates a premature translational stop signal (p.Tyr189*) 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).

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: May 1, 2024

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