RMC1
protein-codingregulator of MON1-CCZ1, the group of WD repeat domain containing
Gene summary
This gene encodes a colon cancer associated protein. [provided by RefSeq, Jan 2013]
- C18orf8
- WDR98
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~28.3 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to RMC1 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_013326.5. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 3 | 1 | 4 | 8 | ||
| missense | 10 | 1 | 11 | |||
| nonsense | 3 | 3 | ||||
| start loss | 0 | |||||
| frameshift | 1 | 1 | ||||
| splice donor/acceptor (+/-2bp) | 2 | 2 | ||||
| Total | 0 | 0 | 19 | 2 | 4 | 25 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_037458.3 | 20 | MANE Select | |
| Ensembl | ENSP00000269221.2 | 20 | MANE Select | |
| RefSeq | NP_001263271.1 | 18 | Standard | |
| RefSeq | NP_001305636.1 | 15 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- autophagy
- regulation of autophagy
Cellular Component
- lysosomal membrane
- late endosome membrane
- Mon1-Ccz1 complex
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000269221
- Coding exons
- 20
- Length
- 28274
- Individuals with no LoFs
- 125728
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 20
- Defined
- 125748
- p
- 0.0000795
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 1.74 | 281 | 376 | 0.748 | 0.0000208 | 4312 |
| Missense (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 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.000062 | 0.000062 | rare |
| Latino/Admixed American | 0.000058 | 0.000058 | rare |
| Ashkenazi Jewish | 0.00040 | 0.00040 | rare |
| East Asian | 0.00011 | 0.00011 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.000062 | 0.000062 | rare |
| South Asian | 0.00013 | 0.00013 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- 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
Essentials
- Essential (gene trap)
- N