NM_004329.3(BMPR1A):c.349dup (p.Gln117fs) AND Juvenile polyposis syndrome

This record was updated by the submitter. Please see the current version.

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Oct 16, 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:: RCV002877591.2

Allele description

NM_004329.3(BMPR1A):c.349dup (p.Gln117fs)

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.349dup (p.Gln117fs)

HGVS:

NC_000010.11:g.86899809dup
NG_009362.1:g.148171dup
NM_001406559.1:c.349dup
NM_001406560.1:c.349dup
NM_001406561.1:c.349dup
NM_001406562.1:c.349dup
NM_001406563.1:c.349dup
NM_001406564.1:c.349dup
NM_001406565.1:c.349dup
NM_001406566.1:c.349dup
NM_001406567.1:c.349dup
NM_001406568.1:c.349dup
NM_001406569.1:c.349dup
NM_001406570.1:c.349dup
NM_001406571.1:c.349dup
NM_001406572.1:c.349dup
NM_001406573.1:c.349dup
NM_001406574.1:c.349dup
NM_001406575.1:c.349dup
NM_001406576.1:c.349dup
NM_001406577.1:c.349dup
NM_001406578.1:c.349dup
NM_001406579.1:c.349dup
NM_001406580.1:c.349dup
NM_001406581.1:c.349dup
NM_001406582.1:c.349dup
NM_001406583.1:c.349dup
NM_001406584.1:c.265dup
NM_001406585.1:c.265dup
NM_001406586.1:c.265dup
NM_001406587.1:c.265dup
NM_001406588.1:c.265dup
NM_004329.3:c.349dupMANE SELECT
NP_001393488.1:p.Gln117Profs
NP_001393489.1:p.Gln117Profs
NP_001393490.1:p.Gln117Profs
NP_001393491.1:p.Gln117Profs
NP_001393492.1:p.Gln117Profs
NP_001393493.1:p.Gln117Profs
NP_001393494.1:p.Gln117Profs
NP_001393495.1:p.Gln117Profs
NP_001393496.1:p.Gln117Profs
NP_001393497.1:p.Gln117Profs
NP_001393498.1:p.Gln117Profs
NP_001393499.1:p.Gln117Profs
NP_001393500.1:p.Gln117Profs
NP_001393501.1:p.Gln117Profs
NP_001393502.1:p.Gln117Profs
NP_001393503.1:p.Gln117Profs
NP_001393504.1:p.Gln117Profs
NP_001393505.1:p.Gln117Profs
NP_001393506.1:p.Gln117Profs
NP_001393507.1:p.Gln117Profs
NP_001393508.1:p.Gln117Profs
NP_001393509.1:p.Gln117Profs
NP_001393510.1:p.Gln117Profs
NP_001393511.1:p.Gln117Profs
NP_001393512.1:p.Gln117Profs
NP_001393513.1:p.Gln89Profs
NP_001393514.1:p.Gln89Profs
NP_001393515.1:p.Gln89Profs
NP_001393516.1:p.Gln89Profs
NP_001393517.1:p.Gln89Profs
NP_004320.2:p.Gln117Profs
NP_004320.2:p.Gln117fs
LRG_298t1:c.349dup
LRG_298:g.148171dup
LRG_298p1:p.Gln117Profs
NC_000010.10:g.88659563_88659564insC
NC_000010.10:g.88659566dup
NM_004329.2:c.349dup
NR_176211.1:n.917dup
NR_176212.1:n.917dup
NR_176213.1:n.917dup

Protein change:

Q117fs

Molecular consequence:

NM_001406559.1:c.349dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406560.1:c.349dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406561.1:c.349dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406562.1:c.349dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406563.1:c.349dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406564.1:c.349dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406565.1:c.349dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406566.1:c.349dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406567.1:c.349dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406568.1:c.349dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406569.1:c.349dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406570.1:c.349dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406571.1:c.349dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406572.1:c.349dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406573.1:c.349dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406574.1:c.349dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406575.1:c.349dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406576.1:c.349dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406577.1:c.349dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406578.1:c.349dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406579.1:c.349dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406580.1:c.349dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406581.1:c.349dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406582.1:c.349dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406583.1:c.349dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406584.1:c.265dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406585.1:c.265dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406586.1:c.265dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406587.1:c.265dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406588.1:c.265dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_004329.3:c.349dup - 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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Combined oxidative phosphorylation deficiency 56
Combined oxidative phosphorylation deficiency 56

MedGen
C5774261[conceptid] (1)
MedGen
RPB1, partial [Cortinarius erythrocephalus]
RPB1, partial [Cortinarius erythrocephalus]
gi|409107675|gb|AFV13196.1|

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003236940	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Oct 16, 2022)	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

SCV003236940

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Oct 16, 2022)

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, SCV003236940.2

#	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. 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.Gln117Profs*15) 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 20, 2024

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