NM_004329.3(BMPR1A):c.1138G>C (p.Asp380His) AND Juvenile polyposis syndrome

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

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jan 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:: RCV003879430.1

Allele description

NM_004329.3(BMPR1A):c.1138G>C (p.Asp380His)

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.1138G>C (p.Asp380His)

HGVS:

NC_000010.11:g.86919441G>C
NG_009362.1:g.167803G>C
NM_001406559.1:c.1213G>C
NM_001406560.1:c.1186G>C
NM_001406561.1:c.1138G>C
NM_001406562.1:c.1138G>C
NM_001406563.1:c.1138G>C
NM_001406564.1:c.1138G>C
NM_001406565.1:c.1138G>C
NM_001406566.1:c.1138G>C
NM_001406567.1:c.1138G>C
NM_001406568.1:c.1138G>C
NM_001406569.1:c.1138G>C
NM_001406570.1:c.1138G>C
NM_001406571.1:c.1138G>C
NM_001406572.1:c.1138G>C
NM_001406573.1:c.1138G>C
NM_001406574.1:c.1138G>C
NM_001406575.1:c.1138G>C
NM_001406576.1:c.1138G>C
NM_001406577.1:c.1138G>C
NM_001406578.1:c.1138G>C
NM_001406579.1:c.1138G>C
NM_001406580.1:c.1138G>C
NM_001406581.1:c.1138G>C
NM_001406582.1:c.1138G>C
NM_001406583.1:c.1132G>C
NM_001406584.1:c.1054G>C
NM_001406585.1:c.1054G>C
NM_001406586.1:c.1054G>C
NM_001406587.1:c.1054G>C
NM_001406588.1:c.1054G>C
NM_001406589.1:c.796G>C
NM_004329.3:c.1138G>CMANE SELECT
NP_001393488.1:p.Asp405His
NP_001393489.1:p.Asp396His
NP_001393490.1:p.Asp380His
NP_001393491.1:p.Asp380His
NP_001393492.1:p.Asp380His
NP_001393493.1:p.Asp380His
NP_001393494.1:p.Asp380His
NP_001393495.1:p.Asp380His
NP_001393496.1:p.Asp380His
NP_001393497.1:p.Asp380His
NP_001393498.1:p.Asp380His
NP_001393499.1:p.Asp380His
NP_001393500.1:p.Asp380His
NP_001393501.1:p.Asp380His
NP_001393502.1:p.Asp380His
NP_001393503.1:p.Asp380His
NP_001393504.1:p.Asp380His
NP_001393505.1:p.Asp380His
NP_001393506.1:p.Asp380His
NP_001393507.1:p.Asp380His
NP_001393508.1:p.Asp380His
NP_001393509.1:p.Asp380His
NP_001393510.1:p.Asp380His
NP_001393511.1:p.Asp380His
NP_001393512.1:p.Asp378His
NP_001393513.1:p.Asp352His
NP_001393514.1:p.Asp352His
NP_001393515.1:p.Asp352His
NP_001393516.1:p.Asp352His
NP_001393517.1:p.Asp352His
NP_001393518.1:p.Asp266His
NP_004320.2:p.Asp380His
NP_004320.2:p.Asp380His
LRG_298t1:c.1138G>C
LRG_298:g.167803G>C
LRG_298p1:p.Asp380His
NC_000010.10:g.88679198G>C
NM_004329.2:c.1138G>C
NR_176211.1:n.1706G>C
NR_176212.1:n.1706G>C
NR_176213.1:n.1706G>C

Protein change:

D266H

Molecular consequence:

NM_001406559.1:c.1213G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001406560.1:c.1186G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001406561.1:c.1138G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001406562.1:c.1138G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001406563.1:c.1138G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001406564.1:c.1138G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001406565.1:c.1138G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001406566.1:c.1138G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001406567.1:c.1138G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001406568.1:c.1138G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001406569.1:c.1138G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001406570.1:c.1138G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001406571.1:c.1138G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001406572.1:c.1138G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001406573.1:c.1138G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001406574.1:c.1138G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001406575.1:c.1138G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001406576.1:c.1138G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001406577.1:c.1138G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001406578.1:c.1138G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001406579.1:c.1138G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001406580.1:c.1138G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001406581.1:c.1138G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001406582.1:c.1138G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001406583.1:c.1132G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001406584.1:c.1054G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001406585.1:c.1054G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001406586.1:c.1054G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001406587.1:c.1054G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001406588.1:c.1054G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001406589.1:c.796G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_004329.3:c.1138G>C - missense variant - [Sequence Ontology: SO:0001583]
NR_176211.1:n.1706G>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_176212.1:n.1706G>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_176213.1:n.1706G>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]

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
SCV004683550	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Jan 1, 2023)	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

SCV004683550

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Jan 1, 2023)

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. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Invitae, SCV004683550.1

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

Description

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. Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be disruptive. 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 replaces aspartic acid, which is acidic and polar, with histidine, which is basic and polar, at codon 380 of the BMPR1A protein (p.Asp380His).

#	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: Mar 5, 2024

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