NM_004329.3(BMPR1A):c.258AGA[2] (p.Glu88del) AND Juvenile polyposis syndrome

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Dec 11, 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:: RCV002228959.12

Allele description [Variation Report for NM_004329.3(BMPR1A):c.258AGA[2] (p.Glu88del)]

NM_004329.3(BMPR1A):c.258AGA[2] (p.Glu88del)

Gene:

BMPR1A:bone morphogenetic protein receptor type 1A [Gene - OMIM - HGNC]

Variant type:

Microsatellite

Cytogenetic location:

10q23.2

Genomic location:

Preferred name:

NM_004329.3(BMPR1A):c.258AGA[2] (p.Glu88del)

HGVS:

NC_000010.11:g.86892154AGA[2]
NG_009362.1:g.140516AGA[2]
NM_004329.3:c.258AGA[2]MANE SELECT
NP_004320.2:p.Glu88del
LRG_298:g.140516AGA[2]
NC_000010.10:g.88651911AGA[2]
NC_000010.10:g.88651911_88651913del
NM_004329.2:c.264_266delAGA

Protein change:

E88del

Links:

dbSNP: rs876659086

NCBI 1000 Genomes Browser:

rs876659086

Molecular consequence:

NM_004329.3:c.258AGA[2] - inframe_deletion - [Sequence Ontology: SO:0001822]

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
SCV000941716	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Dec 11, 2023)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 21640116, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000941716

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Dec 11, 2023)

germline

clinical testing

PubMed (2)
[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

BMPR1A mutations in hereditary nonpolyposis colorectal cancer without mismatch repair deficiency.

Nieminen TT, Abdel-Rahman WM, Ristimäki A, Lappalainen M, Lahermo P, Mecklin JP, Järvinen HJ, Peltomäki P.

Gastroenterology. 2011 Jul;141(1):e23-6. doi: 10.1053/j.gastro.2011.03.063. Epub 2011 Jun 1. No abstract available.

PubMed [citation]

PMID:: 21640116

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 Labcorp Genetics (formerly Invitae), Labcorp, SCV000941716.4

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (2)

Description

This variant, c.264_266del, results in the deletion of 1 amino acid(s) of the BMPR1A protein (p.Glu88del), but otherwise preserves the integrity of the reading frame. This variant is present in population databases (rs771235294, gnomAD 0.0009%). This variant has been observed in individual(s) with colorectal cancer (PMID: 21640116). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 231317). Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. 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: Nov 3, 2024

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