NM_001203.3(BMPR1B):c.47A>G (p.Glu16Gly) AND multiple conditions

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

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Apr 22, 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:: RCV003799556.1

Allele description

NM_001203.3(BMPR1B):c.47A>G (p.Glu16Gly)

Gene:

BMPR1B:bone morphogenetic protein receptor type 1B [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

4q22.3

Genomic location:

Preferred name:

NM_001203.3(BMPR1B):c.47A>G (p.Glu16Gly)

HGVS:

NC_000004.12:g.95104471A>G
NG_009245.1:g.351495A>G
NM_001203.3:c.47A>GMANE SELECT
NM_001256792.2:c.47A>G
NM_001256793.2:c.137A>G
NM_001256794.1:c.47A>G
NP_001194.1:p.Glu16Gly
NP_001243721.1:p.Glu16Gly
NP_001243722.1:p.Glu46Gly
NP_001243723.1:p.Glu16Gly
NC_000004.11:g.96025622A>G

Protein change:

E16G

Molecular consequence:

NM_001203.3:c.47A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001256792.2:c.47A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001256793.2:c.137A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001256794.1:c.47A>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Type A2 brachydactyly (BDA2)
Synonyms:: BRACHYMESOPHALANGY II; Mohr-Wriedt type brachydactyly; Brachydactyly, type 2a; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0007216; MedGen: C1832702; Orphanet: 93396; OMIM: 112600; Human Phenotype Ontology: HP:0009372

Name:: Acromesomelic dysplasia 3 (AMD3)
Synonyms:: Chondrodysplasia acromesomelic with genital anomalies; CHONDRODYSPLASIA, ACROMESOMELIC, WITH OR WITHOUT GENITAL ANOMALIES; Acromesomelic dysplasia, Demirhan type
Identifiers:: MONDO: MONDO:0012274; MedGen: C4225404; OMIM: 609441

Recent activity

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predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
gi|219115711|ref|XP_002178651.1|

Protein
Uloma sp. 3 GJK-2014 voucher LSOL.02242 16S ribosomal RNA gene, partial sequence...
Uloma sp. 3 GJK-2014 voucher LSOL.02242 16S ribosomal RNA gene, partial sequence; mitochondrial
gi|630605919|gb|KJ510106.1|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004585146	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Apr 22, 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

SCV004585146

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Apr 22, 2023)

germline

clinical testing

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

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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, SCV004585146.1

#	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. 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 BMPR1B protein function. This variant has not been reported in the literature in individuals affected with BMPR1B-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change replaces glutamic acid, which is acidic and polar, with glycine, which is neutral and non-polar, at codon 16 of the BMPR1B protein (p.Glu16Gly).

#	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: Apr 15, 2024

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