RMC1

regulator of MON1-CCZ1, the group of WD repeat domain containing

Basic information

Region (hg38): 18:23503469-23531822

Previous symbols: [ "C18orf8", "WDR98" ]

Links

ENSG00000141452 ∙ NCBI:29919 ∙ OMIM:620267 ∙ HGNC:24326 ∙ Uniprot:Q96DM3 ∙ 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 RMC1 gene.

• not provided (7 variants)
• Niemann-Pick disease, type C1 (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RMC1 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	4	5
missense				1		1
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			1	1		2
Total	0	0	1	3	4

Variants in RMC1

This is a list of pathogenic ClinVar variants found in the RMC1 region.

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

Position	Type	Phenotype	Significance	ClinVar
18-23503675-G-T		not specified	Uncertain significance (Aug 16, 2021)
18-23503683-C-A			Likely benign (Aug 05, 2018)
18-23504412-T-G			Likely benign (Apr 06, 2018)
18-23515960-G-A			Benign (Jul 15, 2018)
18-23515989-A-G		not specified	Uncertain significance (Sep 17, 2021)
18-23516323-G-T		not specified	Uncertain significance (Aug 10, 2021)
18-23516432-G-A			Likely benign (Jul 15, 2018)
18-23518925-A-G		not specified	Uncertain significance (Jul 20, 2021)
18-23526674-A-C			Benign (Apr 09, 2018)
18-23527835-C-G			Benign (Jun 13, 2018)
18-23527897-C-T		not specified	Uncertain significance (Sep 01, 2021)
18-23529669-T-C		not specified	Uncertain significance (Nov 08, 2021)
18-23530033-C-T			Benign (Mar 29, 2018)
18-23531484-G-A		Niemann-Pick disease, type C1	Uncertain significance (Jan 12, 2018)
18-23531702-T-C		Niemann-Pick disease, type C1	Uncertain significance (Jan 12, 2018)
18-23531708-C-A		Niemann-Pick disease, type C1	Uncertain significance (Jan 13, 2018)
18-23531716-G-GT		Niemann-Pick disease, type C	Uncertain significance (Jun 14, 2016)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RMC1	protein_coding	protein_coding	ENST00000269221	20	28274

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.988	0.0118	125728	0	20	125748	0.0000795

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.74	281	376	0.748	0.0000208	4312
Missense in Polyphen		46	90.082	0.51065		1055
Synonymous	0.345	142	147	0.964	0.00000892	1225
Loss of Function	5.19	7	44.3	0.158	0.00000253	477

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000120	0.000120
Ashkenazi Jewish	0.000397	0.000397
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000616	0.0000615
Middle Eastern	0.000109	0.000109
South Asian	0.000131	0.000131
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Componement of the CCZ1-MON1 RAB7A guanine exchange factor (GEF). Acts as a positive regulator of CCZ1-MON1A/B function necessary for endosomal/autophagic flux and efficient RAB7A localization (PubMed:29038162). {ECO:0000269|PubMed:29038162}.

Intolerance Scores

• rvis_EVS: -0.13
• rvis_percentile_EVS: 43.91

Haploinsufficiency Scores

• pHI: 0.0897
• hipred: Y
• hipred_score: 0.728
• ghis: 0.480

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Rmc1

Gene ontology

• Biological process: autophagy;regulation of autophagy
• Cellular component: lysosomal membrane;late endosome membrane;Mon1-Ccz1 complex