NM_004329.3(BMPR1A):c.338del (p.Ser113fs) AND Juvenile polyposis syndrome

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Mar 21, 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:: RCV002837950.2

Allele description [Variation Report for NM_004329.3(BMPR1A):c.338del (p.Ser113fs)]

NM_004329.3(BMPR1A):c.338del (p.Ser113fs)

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.338del (p.Ser113fs)

HGVS:

NC_000010.11:g.86899798del
NG_009362.1:g.148160del
NM_001406559.1:c.338delC
NM_001406560.1:c.338delC
NM_001406561.1:c.338delC
NM_001406562.1:c.338delC
NM_001406563.1:c.338delC
NM_001406564.1:c.338delC
NM_001406565.1:c.338delC
NM_001406566.1:c.338delC
NM_001406567.1:c.338delC
NM_001406568.1:c.338delC
NM_001406569.1:c.338delC
NM_001406570.1:c.338delC
NM_001406571.1:c.338delC
NM_001406572.1:c.338delC
NM_001406573.1:c.338delC
NM_001406574.1:c.338delC
NM_001406575.1:c.338delC
NM_001406576.1:c.338delC
NM_001406577.1:c.338delC
NM_001406578.1:c.338delC
NM_001406579.1:c.338delC
NM_001406580.1:c.338delC
NM_001406581.1:c.338delC
NM_001406582.1:c.338delC
NM_001406583.1:c.338delC
NM_001406584.1:c.254delC
NM_001406585.1:c.254delC
NM_001406586.1:c.254delC
NM_001406587.1:c.254delC
NM_001406588.1:c.254delC
NM_004329.3:c.338delMANE SELECT
NP_001393488.1:p.Ser113Phefs
NP_001393489.1:p.Ser113Phefs
NP_001393490.1:p.Ser113Phefs
NP_001393491.1:p.Ser113Phefs
NP_001393492.1:p.Ser113Phefs
NP_001393493.1:p.Ser113Phefs
NP_001393494.1:p.Ser113Phefs
NP_001393495.1:p.Ser113Phefs
NP_001393496.1:p.Ser113Phefs
NP_001393497.1:p.Ser113Phefs
NP_001393498.1:p.Ser113Phefs
NP_001393499.1:p.Ser113Phefs
NP_001393500.1:p.Ser113Phefs
NP_001393501.1:p.Ser113Phefs
NP_001393502.1:p.Ser113Phefs
NP_001393503.1:p.Ser113Phefs
NP_001393504.1:p.Ser113Phefs
NP_001393505.1:p.Ser113Phefs
NP_001393506.1:p.Ser113Phefs
NP_001393507.1:p.Ser113Phefs
NP_001393508.1:p.Ser113Phefs
NP_001393509.1:p.Ser113Phefs
NP_001393510.1:p.Ser113Phefs
NP_001393511.1:p.Ser113Phefs
NP_001393512.1:p.Ser113Phefs
NP_001393513.1:p.Ser85Phefs
NP_001393514.1:p.Ser85Phefs
NP_001393515.1:p.Ser85Phefs
NP_001393516.1:p.Ser85Phefs
NP_001393517.1:p.Ser85Phefs
NP_004320.2:p.Ser113Phefs
NP_004320.2:p.Ser113fs
LRG_298t1:c.338del
LRG_298:g.148160del
LRG_298p1:p.Ser113Phefs
NC_000010.10:g.88659555del
NM_004329.2:c.338delC
NR_176211.1:n.906delC
NR_176212.1:n.906delC
NR_176213.1:n.906delC

Protein change:

S113fs

Molecular consequence:

NM_001406559.1:c.338delC - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406560.1:c.338delC - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406561.1:c.338delC - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406562.1:c.338delC - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406563.1:c.338delC - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406564.1:c.338delC - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406565.1:c.338delC - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406566.1:c.338delC - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406567.1:c.338delC - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406568.1:c.338delC - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406569.1:c.338delC - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406570.1:c.338delC - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406571.1:c.338delC - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406572.1:c.338delC - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406573.1:c.338delC - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406574.1:c.338delC - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406575.1:c.338delC - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406576.1:c.338delC - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406577.1:c.338delC - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406578.1:c.338delC - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406579.1:c.338delC - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406580.1:c.338delC - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406581.1:c.338delC - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406582.1:c.338delC - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406583.1:c.338delC - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406584.1:c.254delC - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406585.1:c.254delC - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406586.1:c.254delC - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406587.1:c.254delC - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406588.1:c.254delC - frameshift variant - [Sequence Ontology: SO:0001589]
NM_004329.3:c.338del - frameshift variant - [Sequence Ontology: SO:0001589]

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
SCV003208650	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Mar 21, 2023)	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

SCV003208650

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Mar 21, 2023)

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 Invitae, SCV003208650.2

#	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. ClinVar contains an entry for this variant (Variation ID: 2006853). 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 creates a premature translational stop signal (p.Ser113Phefs*10) 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: Feb 28, 2024

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