RMC1
Basic information
Region (hg38): 18:23503496-23531822
Previous symbols: [ "C18orf8", "WDR98" ]
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
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 | 5 | |||||
missense | 7 | |||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
splice region | 0 | |||||
non coding | 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) | ||
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) | ||
18-23524186-T-A | not specified | Likely benign (May 10, 2024) | ||
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:
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:
- 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