CLVS1
Basic information
Region (hg38): 8:61057158-61501645
Previous symbols: [ "RLBP1L1" ]
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 CLVS1 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 | 0 | |||||
| missense | 9 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 1 | |||||
| Total | 0 | 0 | 10 | 0 | 0 |
Variants in CLVS1
This is a list of pathogenic ClinVar variants found in the CLVS1 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 8-61299927-A-G | not specified | Uncertain significance (May 13, 2024) | ||
| 8-61299931-T-C | not specified | Uncertain significance (Dec 26, 2023) | ||
| 8-61299952-T-C | not specified | Uncertain significance (Oct 13, 2023) | ||
| 8-61299989-G-T | not specified | Uncertain significance (Nov 15, 2021) | ||
| 8-61300143-G-A | not specified | Uncertain significance (Dec 19, 2023) | ||
| 8-61376667-C-T | not specified | Uncertain significance (Nov 27, 2023) | ||
| 8-61376682-A-G | not specified | Uncertain significance (Mar 21, 2024) | ||
| 8-61376745-C-T | not specified | Uncertain significance (Jun 13, 2024) | ||
| 8-61454181-A-G | not specified | Uncertain significance (Sep 01, 2021) | ||
| 8-61454213-C-T | not specified | Uncertain significance (Apr 27, 2023) | ||
| 8-61458343-C-G | not specified | Uncertain significance (Aug 08, 2023) | ||
| 8-61458422-C-T | not specified | Uncertain significance (Jan 04, 2022) | ||
| 8-61458436-G-A | not specified | Uncertain significance (Sep 29, 2023) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| CLVS1 | protein_coding | protein_coding | ENST00000519846 | 5 | 444488 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.854 | 0.146 | 125725 | 0 | 8 | 125733 | 0.0000318 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.41 | 146 | 203 | 0.720 | 0.0000112 | 2335 |
| Missense in Polyphen | 27 | 64.114 | 0.42112 | 767 | ||
| Synonymous | 0.0111 | 81 | 81.1 | 0.998 | 0.00000487 | 683 |
| Loss of Function | 3.12 | 2 | 15.1 | 0.133 | 8.09e-7 | 175 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000185 | 0.000185 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.0000463 | 0.0000462 |
| European (Non-Finnish) | 0.0000353 | 0.0000352 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Required for normal morphology of late endosomes and/or lysosomes in neurons (By similarity). Binds phosphatidylinositol 3,5-bisphosphate (PtdIns(3,5)P2). {ECO:0000250, ECO:0000269|PubMed:19651769}.;
- Pathway
- Ectoderm Differentiation;Lysosome Vesicle Biogenesis;Clathrin derived vesicle budding;trans-Golgi Network Vesicle Budding;Vesicle-mediated transport;Membrane Trafficking
(Consensus)
Intolerance Scores
- loftool
- 0.0763
- rvis_EVS
- -0.49
- rvis_percentile_EVS
- 22.09
Haploinsufficiency Scores
- pHI
- 0.649
- hipred
- Y
- hipred_score
- 0.654
- ghis
- 0.637
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.231
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Clvs1
- Phenotype
- behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); skeleton phenotype; growth/size/body region phenotype; homeostasis/metabolism phenotype;
Gene ontology
- Biological process
- lysosome organization
- Cellular component
- endosome;trans-Golgi network;clathrin-coated vesicle;early endosome membrane;trans-Golgi network membrane
- Molecular function
- phosphatidylinositol-3,5-bisphosphate binding