RGMA

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

Basic information

Region (hg38): 15:93035270-93089211

Links

ENSG00000182175 ∙ NCBI:56963 ∙ OMIM:607362 ∙ HGNC:30308 ∙ Uniprot:Q96B86 ∙ 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 RGMA gene.

• Inborn genetic diseases (29 variants)
• not provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RGMA 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					1	1
missense			25	2		27
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			2		1	3
Total	0	0	27	2	2

Variants in RGMA

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

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

Position	Type	Phenotype	Significance	ClinVar
15-93045029-G-A		not specified	Likely benign (Dec 05, 2022)
15-93045033-C-T		not specified	Likely benign (Jan 23, 2023)
15-93045053-C-A		not specified	Uncertain significance (Jan 03, 2024)
15-93045113-A-G		not specified	Uncertain significance (Mar 31, 2023)
15-93045185-T-C		not specified	Uncertain significance (Jun 07, 2023)
15-93045293-T-C		not specified	Uncertain significance (Aug 30, 2022)
15-93045294-C-T		not specified	Uncertain significance (Apr 26, 2023)
15-93045314-C-A		not specified	Uncertain significance (Sep 16, 2021)
15-93045381-G-C		not specified	Uncertain significance (Aug 21, 2023)
15-93045427-G-A			Benign (Dec 31, 2019)
15-93045597-C-T		not specified	Uncertain significance (Dec 20, 2023)
15-93045603-C-T		not specified	Uncertain significance (Aug 16, 2022)
15-93045640-G-C		not specified	Uncertain significance (Dec 13, 2022)
15-93045645-T-C		not specified	Uncertain significance (Feb 03, 2022)
15-93052019-C-T		not specified	Uncertain significance (Sep 27, 2021)
15-93052108-C-T		not specified	Uncertain significance (Nov 22, 2022)
15-93052123-C-T		not specified	Uncertain significance (Jan 23, 2023)
15-93052156-G-A		not specified	Uncertain significance (Aug 16, 2021)
15-93052174-G-A		not specified	Uncertain significance (Apr 27, 2022)
15-93052255-G-A		not specified	Uncertain significance (Mar 01, 2023)
15-93052267-G-A		not specified	Uncertain significance (Apr 07, 2023)
15-93052322-T-C		not specified	Uncertain significance (May 27, 2022)
15-93052331-C-T		not specified	Uncertain significance (Nov 09, 2021)
15-93052418-C-T		not specified	Uncertain significance (Mar 06, 2023)
15-93052484-T-G		not specified	Uncertain significance (Jan 17, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RGMA	protein_coding	protein_coding	ENST00000557301	4	45798

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.165	0.833	124499	0	6	124505	0.0000241

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.995	255	304	0.839	0.0000205	2907
Missense in Polyphen		83	130.58	0.6356		1285
Synonymous	-0.875	153	140	1.09	0.0000110	942
Loss of Function	2.61	4	14.9	0.269	7.10e-7	159

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000296	0.0000296
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000488	0.0000464
European (Non-Finnish)	0.0000364	0.0000355
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Member of the repulsive guidance molecule (RGM) family that performs several functions in the developing and adult nervous system. Regulates cephalic neural tube closure, inhibits neurite outgrowth and cortical neuron branching, and the formation of mature synapses. Binding to its receptor NEO1/neogenin induces activation of RHOA-ROCK1/Rho-kinase signaling pathway through UNC5B-ARHGEF12/LARG-PTK2/FAK1 cascade, leading to collapse of the neuronal growth cone and neurite outgrowth inhibition. Furthermore, RGMA binding to NEO1/neogenin leads to HRAS inactivation by influencing HRAS-PTK2/FAK1-AKT1 pathway. It also functions as a bone morphogenetic protein (BMP) coreceptor that may signal through SMAD1, SMAD5, and SMAD8. {ECO:0000269|PubMed:19273616, ECO:0000269|PubMed:19458235}.
• Pathway: Spinal Cord Injury;Ectoderm Differentiation;Developmental Biology;BMP receptor signaling;Netrin-1 signaling;Axon guidance (Consensus)

Recessive Scores

• pRec: 0.182

Intolerance Scores

• loftool: 0.0440
• rvis_EVS: -0.64
• rvis_percentile_EVS: 16.63

Haploinsufficiency Scores

• pHI: 0.729
• hipred: N
• hipred_score: 0.278
• ghis: 0.612

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.617

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rgma
• Phenotype: craniofacial 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); embryo phenotype; skeleton 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)

Zebrafish Information Network

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

Gene ontology

• Biological process: BMP signaling pathway;positive regulation of transcription by RNA polymerase II;negative regulation of axon regeneration
• Cellular component: endoplasmic reticulum;plasma membrane;anchored component of membrane
• Molecular function: protein binding;coreceptor activity;transferrin receptor binding