RGMB

repulsive guidance molecule BMP co-receptor b, the group of Repulsive guidance molecule family

Basic information

Region (hg38): 5:98768650-98798643

Links

ENSG00000174136

∙ NCBI:285704 ∙ OMIM:612687 ∙ HGNC:26896 ∙ Uniprot:Q6NW40 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

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

not_specified (64 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RGMB gene is commonly pathogenic or not. These statistics are base on transcript: NM_001366508.1. 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	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			57 clinvar	6 clinvar		63
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	57	6	0

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RGMB	protein_coding	protein_coding	ENST00000308234	4	29994

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0720	0.917	124638	0	8	124646	0.0000321

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.708	230	262	0.877	0.0000150	3086
Missense in Polyphen		83	120.61	0.68816		1436
Synonymous	-0.224	109	106	1.03	0.00000638	987
Loss of Function	2.21	4	12.4	0.323	6.71e-7	152

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000449	0.0000442
Middle Eastern	0.00	0.00
South Asian	0.0000984	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Function: FUNCTION: Member of the repulsive guidance molecule (RGM) family that contributes to the patterning of the developing nervous system (By similarity). Acts as a bone morphogenetic protein (BMP) coreceptor that potentiates BMP signaling (By similarity). Promotes neuronal adhesion (By similarity). May inhibit neurite outgrowth. {ECO:0000250, ECO:0000269|PubMed:19324014}.;
Pathway: Developmental Biology;BMP receptor signaling;Netrin-1 signaling;Axon guidance (Consensus)

Recessive Scores

pRec: 0.169

Intolerance Scores

loftool: 0.220
rvis_EVS: -0.07
rvis_percentile_EVS: 48.35

Haploinsufficiency Scores

pHI: 0.144
hipred: N
hipred_score: 0.292
ghis: 0.480

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: N
gene_indispensability_score: 0.457

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Rgmb
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);

Zebrafish Information Network

Gene name: rgmb
Affected structure: liver
Phenotype tag: abnormal
Phenotype quality: decreased size

Gene ontology

Biological process: cell adhesion;signal transduction;BMP signaling pathway;positive regulation of transcription, DNA-templated
Cellular component: endoplasmic reticulum-Golgi intermediate compartment;plasma membrane;membrane raft;anchored component of plasma membrane
Molecular function: protein binding;coreceptor activity;identical protein binding