BMPER

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

Basic information

Region (hg38): 7:33904308-34156427

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 (233 variants)
• Inborn_genetic_diseases (99 variants)
• Diaphanospondylodysostosis (60 variants)
• BMPER-related_disorder (8 variants)
• not_specified (4 variants)
• HP:0003549 (1 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. These statistics are base on transcript: NM_001365308.1. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous			1	74	7	82
missense	2	2	154	9	2	169
nonsense	8	2				10
start loss						0
frameshift	3	1				4
splice donor/acceptor (+/-2bp)		2				2
Total	13	7	155	83	9

Highest pathogenic variant AF is 0.000015489333

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
		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

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

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