10-86917140-C-T

Variant names:

• chr10-86917140-C-T
• rs587782682
• NM_004329.3:c.682C>T

Variant summary

Our verdict is Pathogenic. Variant got 18 ACMG points: 18P and 0B. PVS1 PM2 PP5_Very_Strong

The NM_004329.3(BMPR1A):​c.682C>T​(p.Arg228*) variant causes a stop gained change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (★★). Variant results in nonsense mediated mRNA decay.

• Frequency: Genomes: not found (cov: 32)
• Consequence: BMPR1A NM_004329.3 stop_gained
• Clinical Significance: Pathogenic criteria provided, multiple submitters, no conflicts P:7 O:1
• Conservation: PhyloP100: 5.01

Genes affected

BMPR1A (HGNC:1076): (bone morphogenetic protein receptor type 1A) The bone morphogenetic protein (BMP) receptors are a family of transmembrane serine/threonine kinases that include the type I receptors BMPR1A and BMPR1B and the type II receptor BMPR2. These receptors are also closely related to the activin receptors, ACVR1 and ACVR2. The ligands of these receptors are members of the TGF-beta superfamily. TGF-betas and activins transduce their signals through the formation of heteromeric complexes with 2 different types of serine (threonine) kinase receptors: type I receptors of about 50-55 kD and type II receptors of about 70-80 kD. Type II receptors bind ligands in the absence of type I receptors, but they require their respective type I receptors for signaling, whereas type I receptors require their respective type II receptors for ligand binding. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Pathogenic. Variant got 18 ACMG points.

• PVS1: Loss of function variant, product undergoes nonsense mediated mRNA decay. LoF is a known mechanism of disease.
• PM2: Very rare variant in population databases, with high coverage
• PP5: Variant 10-86917140-C-T is Pathogenic according to our data. Variant chr10-86917140-C-T is described in ClinVar as [Pathogenic]. Clinvar id is 142735.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr10-86917140-C-T is described in Lovd as [Pathogenic]. Variant chr10-86917140-C-T is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BMPR1A	NM_004329.3	c.682C>T	p.Arg228*	stop_gained	Exon 9 of 13	ENST00000372037.8	NP_004320.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BMPR1A	ENST00000372037.8	c.682C>T	p.Arg228*	stop_gained	Exon 9 of 13	1	NM_004329.3	ENSP00000361107.2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 32

GnomAD4 genome Cov.: 32

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:7 Other:1

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Hereditary cancer-predisposing syndrome Pathogenic:2

Nov 30, 2023

Ambry Genetics

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The p.R228* pathogenic mutation (also known as c.682C>T), located in coding exon 7 of the BMPR1A gene, results from a C to T substitution at nucleotide position 682. This changes the amino acid from an arginine to a stop codon within coding exon 7. This alteration has been identified in numerous individuals with juvenile polyposis syndrome (JPS) (Aretz S et al. J. Med. Genet. 2007; 44:702-0; Friedl W et al. Hum. Genet. 2002; 111:108-11; Ngeow J et al. Gastroenterology 2013; 144:1402-9, 1409.e1-5). This variant is considered to be rare based on population cohorts in the Genome Aggregation Database (gnomAD). In addition to the clinical data presented in the literature, this alteration is expected to result in loss of function by premature protein truncation or nonsense-mediated mRNA decay. As such, this alteration is interpreted as a disease-causing mutation. -

Nov 16, 2022

Color Diagnostics, LLC DBA Color Health

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant changes 1 nucleotide in exon 9 of the BMPR1A gene, creating a premature translation stop signal. This variant is expected to result in an absent or non-functional protein product. To our knowledge, this variant has been reported in individuals affected with juvenile polyposis syndrome (JPS) in the literature (PMID: 12136244, 17873119, 23399955). This variant has not been identified in the general population by the Genome Aggregation Database (gnomAD). Loss of BMPR1A function is a known mechanism of disease (clinicalgenome.org). Based on the available evidence, this variant is classified as Pathogenic. -

Juvenile polyposis syndrome Pathogenic:2

May 26, 2023

Myriad Genetics, Inc.

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant is considered pathogenic. This variant creates a termination codon and is predicted to result in premature protein truncation. -

Dec 30, 2023

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This sequence change creates a premature translational stop signal (p.Arg228*) in the BMPR1A gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in BMPR1A are known to be pathogenic (PMID: 11536076, 12417513). This variant is not present in population databases (gnomAD no frequency). This premature translational stop signal has been observed in individuals with juvenile polyposis syndrome (PMID: 12136244, 23399955). ClinVar contains an entry for this variant (Variation ID: 142735). For these reasons, this variant has been classified as Pathogenic. -

BMPR1A-Related Polyposis Syndrome Pathogenic:1

Dec 15, 2023

Rady Children's Institute for Genomic Medicine, Rady Children's Hospital San Diego

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This nonsense variant found in exon 9 of 13 is predicted to result in loss of normal protein function through either protein truncation or nonsense-mediated mRNA decay. Loss-of-function variation in BMPR1A is an established mechanism of disease (PMID: 11536076, 12417513). This variant has been previously reported in individuals with juvenile polyposis syndrome (PMID: 12136244, 23399955, 28152038). The c.682C>T (p.Arg228Ter) variant is absent from the gnomAD population database and thus is presumed to be rare. Based on the available evidence, c.682C>T (p.Arg228Ter) is classified as Pathogenic. -

not provided Pathogenic:1

Jan 23, 2024

Quest Diagnostics Nichols Institute San Juan Capistrano

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The BMPR1A c.682C>T (p.Arg228*) variant causes the premature termination of BMPR1A protein synthesis. This variant has been reported in the published literature in affected individuals with Juvenile polyposis syndrome (JPS) (PMIDs: 12136244 (2002), 17873119 (2007), and 23399955 (2013)), as well as in an individual with colorectal cancer (PMID: 34897210 (2022)). This variant has not been reported in large, multi-ethnic general populations (Genome Aggregation Database, http://gnomad.broadinstitute.org). Based on the available information, this variant is classified as pathogenic. -

Generalized juvenile polyposis/juvenile polyposis coli Pathogenic:1

Feb 09, 2017

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Variant summary: The BMPR1A c.682C>T (p.Arg228X) variant results in a premature termination codon, predicted to cause a truncated or absent BMPR1A protein due to nonsense mediated decay, which are commonly known mechanisms for disease. The variant of interest was not observed in controls (ExAC, 1000 Gs, or ESP), however, publications have cited the variant in two affected females with juvenile polyposis syndrome. In addition, multiple clinical diagnostic laboratories classified this variant as pathogenic. Taken together, this variant is classified as pathogenic. -

Neoplasm Other:1

Mar 04, 2025

Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital

Significance: -

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Pathogenic	0.63	D
BayesDel_noAF	Pathogenic	0.66
CADD	Pathogenic	39
DANN	Uncertain	1.0
Eigen	Pathogenic	0.90
Eigen_PC	Pathogenic	0.79
FATHMM_MKL	Pathogenic	0.97	D
Vest4		0.97
GERP RS		5.6

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.090		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs587782682; hg19: chr10-88676897; COSMIC: COSV64408454;