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.

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.

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						0
missense			28	4		32
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	28	4	0

Variants in RGMB

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

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

Position	Type	Phenotype	Significance	ClinVar
5-98774107-G-A		not specified	Uncertain significance (May 30, 2023)
5-98774110-G-T		not specified	Uncertain significance (Apr 15, 2024)
5-98774122-G-A		not specified	Uncertain significance (Jun 16, 2024)
5-98774141-G-A		not specified	Uncertain significance (May 08, 2024)
5-98774144-T-C		not specified	Uncertain significance (Feb 27, 2024)
5-98774150-C-T		not specified	Uncertain significance (Mar 27, 2023)
5-98774153-C-G		not specified	Uncertain significance (Jun 03, 2022)
5-98774155-C-A		not specified	Uncertain significance (Jun 18, 2021)
5-98774158-C-G		not specified	Uncertain significance (May 31, 2023)
5-98779610-T-C		not specified	Uncertain significance (Jan 06, 2023)
5-98779663-G-A		not specified	Likely benign (Aug 28, 2023)
5-98779786-C-T		not specified	Uncertain significance (May 14, 2024)
5-98779789-A-G		not specified	Uncertain significance (May 23, 2023)
5-98779831-A-G		not specified	Uncertain significance (Jan 09, 2024)
5-98779838-C-G		not specified	Uncertain significance (Feb 03, 2022)
5-98779973-A-T		not specified	Uncertain significance (Nov 08, 2022)
5-98780050-C-A		not specified	Uncertain significance (Sep 12, 2023)
5-98793085-A-G		not specified	Uncertain significance (Feb 16, 2023)
5-98793091-A-G		not specified	Uncertain significance (Jul 09, 2021)
5-98793110-A-G		not specified	Likely benign (Feb 16, 2023)
5-98793119-C-T		not specified	Uncertain significance (May 29, 2024)
5-98793121-G-T		not specified	Uncertain significance (Dec 26, 2023)
5-98793158-C-T		not specified	Uncertain significance (Dec 05, 2022)
5-98793319-C-T		not specified	Uncertain significance (May 18, 2023)
5-98793331-G-A		not specified	Uncertain significance (May 22, 2023)

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