BMPER

BMP binding endothelial regulator, the group of Cysteine rich transmembrane BMP regulators

Basic information

Region (hg38): 7:33904307-34156427

Links

ENSG00000164619 ∙ NCBI:168667 ∙ OMIM:608699 ∙ HGNC:24154 ∙ Uniprot:Q8N8U9 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• diaphanospondylodysostosis (Definitive), mode of inheritance: AR
• diaphanospondylodysostosis (Strong), mode of inheritance: AR
• diaphanospondylodysostosis (Supportive), mode of inheritance: AR
• ischio-vertebral syndrome (Supportive), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Diaphanospondylodysostosis	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Craniofacial; Musculoskeletal; Renal	20869035; 30006055

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the BMPER gene.

• not provided (190 variants)
• Diaphanospondylodysostosis (122 variants)
• Inborn genetic diseases (24 variants)
• not specified (4 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the BMPER gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous			2	35	10	47
missense		1	90	3	3	97
nonsense	6	1	1			8
start loss						0
frameshift	1					1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region			5	3	1	9
non coding			47	23	44	114
Total	7	2	140	61	57

Highest pathogenic variant AF is 0.0000131

Variants in BMPER

This is a list of pathogenic ClinVar variants found in the BMPER region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
7-33904923-C-A		Diaphanospondylodysostosis	Likely benign (Jan 12, 2018)
7-33904972-G-C		Diaphanospondylodysostosis	Benign (Jan 12, 2018)
7-33904992-T-C		Diaphanospondylodysostosis	Uncertain significance (Jan 12, 2018)
7-33905022-G-A		Diaphanospondylodysostosis	Benign (Jan 13, 2018)
7-33905055-G-A		Diaphanospondylodysostosis	Benign (Jan 13, 2018)
7-33905074-G-A		Diaphanospondylodysostosis	Benign (Jan 13, 2018)
7-33905084-G-T		Diaphanospondylodysostosis	Uncertain significance (Jan 13, 2018)
7-33905093-G-A		Diaphanospondylodysostosis	Uncertain significance (Jan 13, 2018)
7-33905095-C-T		Diaphanospondylodysostosis	Uncertain significance (Jan 12, 2018)
7-33905125-G-A		Diaphanospondylodysostosis	Uncertain significance (Jan 13, 2018)
7-33905148-A-G		Diaphanospondylodysostosis	Benign (Jan 13, 2018)
7-33905153-T-A		Diaphanospondylodysostosis	Uncertain significance (Jan 12, 2018)
7-33905506-G-A		Diaphanospondylodysostosis	Uncertain significance (Jan 13, 2018)
7-33905589-C-A		Diaphanospondylodysostosis	Benign (Jan 13, 2018)
7-33905613-G-C		BMPER-related disorder	Likely benign (Mar 05, 2019)
7-33905629-G-C			Uncertain significance (Jan 15, 2022)
7-33905631-C-A		BMPER-related disorder	Likely benign (Jan 14, 2024)
7-33905638-G-A			Uncertain significance (Aug 26, 2021)
7-33905639-CTCTGGCTGA-AGACCAGAGCGGCG		Diaphanospondylodysostosis	Pathogenic (Oct 08, 2010)
7-33905649-G-A			Likely benign (Nov 28, 2022)
7-33905659-C-A		Inborn genetic diseases	Uncertain significance (Jun 16, 2023)
7-33905660-G-T		Inborn genetic diseases	Uncertain significance (Feb 16, 2023)
7-33905662-C-T		Inborn genetic diseases	Uncertain significance (Sep 13, 2023)
7-33905673-G-A			Likely benign (Jul 16, 2023)
7-33905682-C-T			Likely benign (Dec 09, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
BMPER	protein_coding	protein_coding	ENST00000297161	15	250962

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
6.59e-7	1.00	125699	0	49	125748	0.000195

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0102	380	381	0.999	0.0000228	4492
Missense in Polyphen		94	118.75	0.79156		1415
Synonymous	0.284	141	145	0.970	0.00000919	1256
Loss of Function	3.21	17	38.5	0.442	0.00000201	455

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000119	0.000119
Ashkenazi Jewish	0.00209	0.00209
East Asian	0.000381	0.000381
Finnish	0.00	0.00
European (Non-Finnish)	0.000123	0.000123
Middle Eastern	0.000381	0.000381
South Asian	0.000131	0.000131
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Inhibitor of bone morphogenetic protein (BMP) function, it may regulate BMP responsiveness of osteoblasts and chondrocytes. {ECO:0000269|PubMed:14766204}.

Recessive Scores

• pRec: 0.131

Intolerance Scores

• loftool: 0.616
• rvis_EVS: 0.07
• rvis_percentile_EVS: 59.11

Haploinsufficiency Scores

• pHI: 0.165
• hipred: Y
• hipred_score: 0.737
• ghis: 0.476

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.261

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Bmper
• Phenotype: craniofacial phenotype; growth/size/body region phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); hearing/vestibular/ear phenotype; limbs/digits/tail phenotype; vision/eye phenotype; renal/urinary system phenotype; skeleton phenotype; embryo phenotype; respiratory system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan)

Zebrafish Information Network

• Gene name: bmper
• Affected structure: blood cell
• Phenotype tag: abnormal
• Phenotype quality: decreased amount

Gene ontology

• Biological process: ureteric bud development;blood vessel endothelial cell proliferation involved in sprouting angiogenesis;regulation of endothelial cell migration;negative regulation of BMP signaling pathway;endothelial cell activation;inner ear development;regulation of pathway-restricted SMAD protein phosphorylation;positive regulation of ERK1 and ERK2 cascade;positive regulation of sprouting angiogenesis
• Cellular component: extracellular space