NM_004329.3(BMPR1A):c.15C>A (p.Tyr5Ter) AND Juvenile polyposis syndrome

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Jul 26, 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:: RCV001853815.4

Allele description [Variation Report for NM_004329.3(BMPR1A):c.15C>A (p.Tyr5Ter)]

NM_004329.3(BMPR1A):c.15C>A (p.Tyr5Ter)

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.15C>A (p.Tyr5Ter)

HGVS:

NC_000010.11:g.86876033C>A
NG_009362.1:g.124395C>A
NM_004329.3:c.15C>AMANE SELECT
NP_004320.2:p.Tyr5Ter
NP_004320.2:p.Tyr5Ter
LRG_298t1:c.15C>A
LRG_298:g.124395C>A
LRG_298p1:p.Tyr5Ter
NC_000010.10:g.88635790C>A
NM_004329.2:c.15C>A

Protein change:

Y5*

Links:

dbSNP: rs1392086533

NCBI 1000 Genomes Browser:

rs1392086533

Molecular consequence:

NM_004329.3:c.15C>A - 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
SCV002122159	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Jul 26, 2021)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 11536076, 12417513, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002122159

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Jul 26, 2021)

germline

clinical testing

PubMed (3)
[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

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 Labcorp Genetics (formerly Invitae), Labcorp, SCV002122159.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (3)

Description

For these reasons, this variant has been classified as Pathogenic. This variant has not been reported in the literature in individuals with BMPR1A-related conditions. ClinVar contains an entry for this variant (Variation ID: 486804). This variant is not present in population databases (ExAC no frequency). This sequence change creates a premature translational stop signal (p.Tyr5*) 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: Sep 29, 2024

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