RMC1

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

Basic information

Region (hg38): 18:23503496-23531822

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

Links

ENSG00000141452NCBI:29919OMIM:620267HGNC:24326Uniprot:Q96DM3AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the RMC1 gene.

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
clinvar
4
clinvar
5
missense
6
clinvar
1
clinvar
7
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
0
non coding
1
clinvar
1
clinvar
2
Total 0 0 7 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)3154775
18-23503683-C-A Likely benign (Aug 05, 2018)708242
18-23504412-T-G Likely benign (Apr 06, 2018)785906
18-23515960-G-A Benign (Jul 15, 2018)786337
18-23515989-A-G not specified Uncertain significance (Sep 17, 2021)3154773
18-23516323-G-T not specified Uncertain significance (Aug 10, 2021)3154774
18-23516432-G-A Likely benign (Jul 15, 2018)734642
18-23518925-A-G not specified Uncertain significance (Jul 20, 2021)3154776
18-23524186-T-A not specified Likely benign (May 10, 2024)3336056
18-23526674-A-C Benign (Apr 09, 2018)730421
18-23527835-C-G Benign (Jun 13, 2018)778149
18-23527897-C-T not specified Uncertain significance (Sep 01, 2021)3154770
18-23529669-T-C not specified Uncertain significance (Nov 08, 2021)3154772
18-23530033-C-T Benign (Mar 29, 2018)781357
18-23531484-G-A Niemann-Pick disease, type C1 Uncertain significance (Jan 12, 2018)891595
18-23531702-T-C Niemann-Pick disease, type C1 Uncertain significance (Jan 12, 2018)326239
18-23531708-C-A Niemann-Pick disease, type C1 Uncertain significance (Jan 13, 2018)891596
18-23531716-G-GT Niemann-Pick disease, type C Uncertain significance (Jun 14, 2016)326240

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
RMC1protein_codingprotein_codingENST00000269221 2028274
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.9880.01181257280201257480.0000795
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense1.742813760.7480.00002084312
Missense in Polyphen4690.0820.510651055
Synonymous0.3451421470.9640.000008921225
Loss of Function5.19744.30.1580.00000253477

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0001200.000120
Ashkenazi Jewish0.0003970.000397
East Asian0.0001090.000109
Finnish0.000.00
European (Non-Finnish)0.00006160.0000615
Middle Eastern0.0001090.000109
South Asian0.0001310.000131
Other0.000.00

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

loftool
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_CRISPR
essential_gene_CRISPR2
essential_gene_gene_trap
N
gene_indispensability_pred
gene_indispensability_score

Mouse Genome Informatics

Gene name
Rmc1
Phenotype

Gene ontology

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