NM_001203.3(BMPR1B):c.247-3T>C AND multiple conditions

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

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jan 21, 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:: RCV003087027.4

Allele description

NM_001203.3(BMPR1B):c.247-3T>C

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.247-3T>C

HGVS:

NC_000004.12:g.95115682T>C
NG_009245.1:g.362706T>C
NM_001203.3:c.247-3T>CMANE SELECT
NM_001256792.2:c.247-3T>C
NM_001256793.2:c.337-3T>C
NM_001256794.1:c.247-3T>C
NC_000004.11:g.96036833T>C

Molecular consequence:

NM_001203.3:c.247-3T>C - intron variant - [Sequence Ontology: SO:0001627]
NM_001256792.2:c.247-3T>C - intron variant - [Sequence Ontology: SO:0001627]
NM_001256793.2:c.337-3T>C - intron variant - [Sequence Ontology: SO:0001627]
NM_001256794.1:c.247-3T>C - intron variant - [Sequence Ontology: SO:0001627]

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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SAMN28943104 (1)
SRA
Mus musculus RIKEN cDNA 1500032L24 gene, mRNA (cDNA clone IMAGE:5684373), comple...
Mus musculus RIKEN cDNA 1500032L24 gene, mRNA (cDNA clone IMAGE:5684373), complete cds
gi|61402372|gb|BC092006.1|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003486076	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Jan 21, 2022)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 17576681, 9536098, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003486076

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Jan 21, 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

Aberrant 5' splice sites in human disease genes: mutation pattern, nucleotide structure and comparison of computational tools that predict their utilization.

Buratti E, Chivers M, Královicová J, Romano M, Baralle M, Krainer AR, Vorechovsky I.

Nucleic Acids Res. 2007;35(13):4250-63. Epub 2007 Jun 18.

PubMed [citation]

PMID:: 17576681
PMCID:: PMC1934990

Statistical features of human exons and their flanking regions.

Zhang MQ.

Hum Mol Genet. 1998 May;7(5):919-32.

PubMed [citation]

PMID:: 9536098

See all PubMed Citations (3)

Details of each submission

From Invitae, SCV003486076.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (3)

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. Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant is not likely to affect RNA splicing. This variant has not been reported in the literature in individuals affected with BMPR1B-related conditions. This variant is present in population databases (rs777409748, gnomAD 0.006%). This sequence change falls in intron 5 of the BMPR1B gene. It does not directly change the encoded amino acid sequence of the BMPR1B protein. It affects a nucleotide within the consensus splice site.

#	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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