RND1
Basic information
Region (hg38): 12:48857145-48865870
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 RND1 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 | |||||
| missense | 7 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 7 | 1 | 0 |
Variants in RND1
This is a list of pathogenic ClinVar variants found in the RND1 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 12-48858058-G-T | not specified | Uncertain significance (Sep 12, 2023) | ||
| 12-48858068-G-T | not specified | Uncertain significance (Nov 09, 2021) | ||
| 12-48858081-T-G | not specified | Uncertain significance (May 04, 2022) | ||
| 12-48861004-T-C | not specified | Uncertain significance (Feb 11, 2022) | ||
| 12-48861016-G-A | not specified | Uncertain significance (Feb 10, 2022) | ||
| 12-48861029-G-A | not specified | Uncertain significance (May 14, 2024) | ||
| 12-48865660-A-G | Likely benign (Jan 01, 2020) | |||
| 12-48865673-A-C | not specified | Uncertain significance (Dec 26, 2023) | ||
| 12-48865757-C-A | not specified | Uncertain significance (Mar 05, 2024) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| RND1 | protein_coding | protein_coding | ENST00000309739 | 5 | 8754 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.737 | 0.263 | 125720 | 0 | 3 | 125723 | 0.0000119 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.09 | 101 | 137 | 0.738 | 0.00000763 | 1502 |
| Missense in Polyphen | 47 | 68.722 | 0.68391 | 730 | ||
| Synonymous | 0.507 | 51 | 55.8 | 0.914 | 0.00000316 | 461 |
| Loss of Function | 2.85 | 2 | 13.1 | 0.152 | 8.24e-7 | 137 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000293 | 0.0000293 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000178 | 0.0000176 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Lacks intrinsic GTPase activity. Has a low affinity for GDP, and constitutively binds GTP. Controls rearrangements of the actin cytoskeleton. Induces the Rac-dependent neuritic process formation in part by disruption of the cortical actin filaments. Causes the formation of many neuritic processes from the cell body with disruption of the cortical actin filaments. {ECO:0000269|PubMed:11095956}.;
- Pathway
- Axon guidance - Homo sapiens (human);VEGFA-VEGFR2 Signaling Pathway;Developmental Biology;Sema4D mediated inhibition of cell attachment and migration;Sema4D induced cell migration and growth-cone collapse;Sema4D in semaphorin signaling;SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion;Semaphorin interactions;Axon guidance
(Consensus)
Recessive Scores
- pRec
- 0.165
Intolerance Scores
- loftool
- rvis_EVS
- 0.08
- rvis_percentile_EVS
- 59.76
Haploinsufficiency Scores
- pHI
- 0.227
- hipred
- Y
- hipred_score
- 0.837
- ghis
- 0.407
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.846
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Rnd1
- Phenotype
Gene ontology
- Biological process
- actin filament organization;negative regulation of cell adhesion;Rho protein signal transduction;regulation of cell shape;neuron remodeling;regulation of cell migration;establishment or maintenance of actin cytoskeleton polarity;regulation of actin cytoskeleton organization;actin filament bundle assembly
- Cellular component
- cytoplasm;cytosol;plasma membrane;adherens junction;cell cortex;actin cytoskeleton;cell division site;intracellular membrane-bounded organelle
- Molecular function
- GTPase activity;signaling receptor binding;protein binding;GTP binding;protein kinase binding