RMC1

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

Basic information

Region (hg38): 18:23503496-23531822

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)
• not_specified (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. These statistics are base on transcript: NM_000013326.5. 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	4	5
missense			6	1		7
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	6	2	4

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