NM_004329.3(BMPR1A):c.104T>G (p.Met35Arg) AND Juvenile polyposis syndrome

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Apr 19, 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:: RCV002974878.2

Allele description [Variation Report for NM_004329.3(BMPR1A):c.104T>G (p.Met35Arg)]

NM_004329.3(BMPR1A):c.104T>G (p.Met35Arg)

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.104T>G (p.Met35Arg)

HGVS:

NC_000010.11:g.86890098T>G
NG_009362.1:g.138460T>G
NM_001406559.1:c.104T>G
NM_001406560.1:c.104T>G
NM_001406561.1:c.104T>G
NM_001406562.1:c.104T>G
NM_001406563.1:c.104T>G
NM_001406564.1:c.104T>G
NM_001406565.1:c.104T>G
NM_001406566.1:c.104T>G
NM_001406567.1:c.104T>G
NM_001406568.1:c.104T>G
NM_001406569.1:c.104T>G
NM_001406570.1:c.104T>G
NM_001406571.1:c.104T>G
NM_001406572.1:c.104T>G
NM_001406573.1:c.104T>G
NM_001406574.1:c.104T>G
NM_001406575.1:c.104T>G
NM_001406576.1:c.104T>G
NM_001406577.1:c.104T>G
NM_001406578.1:c.104T>G
NM_001406579.1:c.104T>G
NM_001406580.1:c.104T>G
NM_001406581.1:c.104T>G
NM_001406582.1:c.104T>G
NM_001406583.1:c.104T>G
NM_001406584.1:c.20T>G
NM_001406585.1:c.20T>G
NM_001406586.1:c.20T>G
NM_001406587.1:c.20T>G
NM_001406588.1:c.20T>G
NM_001406589.1:c.104T>G
NM_004329.3:c.104T>GMANE SELECT
NP_001393488.1:p.Met35Arg
NP_001393489.1:p.Met35Arg
NP_001393490.1:p.Met35Arg
NP_001393491.1:p.Met35Arg
NP_001393492.1:p.Met35Arg
NP_001393493.1:p.Met35Arg
NP_001393494.1:p.Met35Arg
NP_001393495.1:p.Met35Arg
NP_001393496.1:p.Met35Arg
NP_001393497.1:p.Met35Arg
NP_001393498.1:p.Met35Arg
NP_001393499.1:p.Met35Arg
NP_001393500.1:p.Met35Arg
NP_001393501.1:p.Met35Arg
NP_001393502.1:p.Met35Arg
NP_001393503.1:p.Met35Arg
NP_001393504.1:p.Met35Arg
NP_001393505.1:p.Met35Arg
NP_001393506.1:p.Met35Arg
NP_001393507.1:p.Met35Arg
NP_001393508.1:p.Met35Arg
NP_001393509.1:p.Met35Arg
NP_001393510.1:p.Met35Arg
NP_001393511.1:p.Met35Arg
NP_001393512.1:p.Met35Arg
NP_001393513.1:p.Met7Arg
NP_001393514.1:p.Met7Arg
NP_001393515.1:p.Met7Arg
NP_001393516.1:p.Met7Arg
NP_001393517.1:p.Met7Arg
NP_001393518.1:p.Met35Arg
NP_004320.2:p.Met35Arg
NP_004320.2:p.Met35Arg
LRG_298t1:c.104T>G
LRG_298:g.138460T>G
LRG_298p1:p.Met35Arg
NC_000010.10:g.88649855T>G
NM_004329.2:c.104T>G
NR_176211.1:n.672T>G
NR_176212.1:n.672T>G
NR_176213.1:n.672T>G

Protein change:

M35R

Molecular consequence:

NM_001406559.1:c.104T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406560.1:c.104T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406561.1:c.104T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406562.1:c.104T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406563.1:c.104T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406564.1:c.104T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406565.1:c.104T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406566.1:c.104T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406567.1:c.104T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406568.1:c.104T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406569.1:c.104T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406570.1:c.104T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406571.1:c.104T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406572.1:c.104T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406573.1:c.104T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406574.1:c.104T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406575.1:c.104T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406576.1:c.104T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406577.1:c.104T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406578.1:c.104T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406579.1:c.104T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406580.1:c.104T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406581.1:c.104T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406582.1:c.104T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406583.1:c.104T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406584.1:c.20T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406585.1:c.20T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406586.1:c.20T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406587.1:c.20T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406588.1:c.20T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406589.1:c.104T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_004329.3:c.104T>G - missense variant - [Sequence Ontology: SO:0001583]

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

Recent activity

Clear Turn Off Turn On

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

Help

Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003281739	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Apr 19, 2022)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003281739

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Apr 19, 2022)

germline

clinical testing

PubMed (1)
[See all records that cite this PMID]

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

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240-242.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Invitae, SCV003281739.2

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

Description

This sequence change replaces methionine, which is neutral and non-polar, with arginine, which is basic and polar, at codon 35 of the BMPR1A protein (p.Met35Arg). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with BMPR1A-related conditions. Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt BMPR1A protein function. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.

#	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 14, 2024

ClinVar

Relating variation to medicine