RO60
Basic information
Region (hg38): 1:193059454-193091777
Previous symbols: [ "SSA2", "TROVE2" ]
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 RO60 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 | 52 | 52 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
splice region | 1 | 1 | ||||
non coding | 0 | |||||
Total | 0 | 0 | 52 | 0 | 1 |
Variants in RO60
This is a list of pathogenic ClinVar variants found in the RO60 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
1-193069078-G-A | not specified | Uncertain significance (Feb 23, 2023) | ||
1-193069139-G-C | not specified | Uncertain significance (Dec 28, 2023) | ||
1-193069140-A-T | not specified | Uncertain significance (Dec 28, 2023) | ||
1-193069188-C-T | not specified | Uncertain significance (Jan 23, 2024) | ||
1-193069211-T-A | not specified | Uncertain significance (Dec 30, 2023) | ||
1-193069322-G-C | not specified | Uncertain significance (Mar 27, 2024) | ||
1-193069364-G-A | not specified | Uncertain significance (Dec 13, 2022) | ||
1-193069427-C-G | not specified | Uncertain significance (Jan 24, 2023) | ||
1-193069456-T-G | not specified | Uncertain significance (May 03, 2023) | ||
1-193069496-C-T | not specified | Uncertain significance (Aug 19, 2024) | ||
1-193069512-C-T | not specified | Uncertain significance (Dec 04, 2024) | ||
1-193069520-T-A | not specified | Uncertain significance (Aug 14, 2024) | ||
1-193069616-C-A | not specified | Uncertain significance (May 20, 2024) | ||
1-193069622-C-G | not specified | Uncertain significance (Dec 04, 2024) | ||
1-193069625-T-G | not specified | Uncertain significance (Mar 15, 2024) | ||
1-193075828-A-G | not specified | Uncertain significance (Aug 02, 2023) | ||
1-193075835-C-A | not specified | Uncertain significance (Aug 27, 2024) | ||
1-193075849-A-G | not specified | Uncertain significance (Apr 29, 2024) | ||
1-193075883-A-C | not specified | Uncertain significance (Dec 14, 2023) | ||
1-193075949-G-T | not specified | Uncertain significance (Aug 26, 2022) | ||
1-193075954-A-G | not specified | Uncertain significance (Nov 28, 2024) | ||
1-193075985-A-G | not specified | Uncertain significance (Dec 15, 2023) | ||
1-193075998-A-C | not specified | Uncertain significance (Apr 07, 2023) | ||
1-193076020-A-C | not specified | Uncertain significance (Mar 19, 2024) | ||
1-193076509-G-A | Benign (May 09, 2018) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
RO60 | protein_coding | protein_coding | ENST00000367446 | 8 | 32356 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.583 | 0.417 | 124750 | 0 | 33 | 124783 | 0.000132 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 1.05 | 240 | 290 | 0.827 | 0.0000147 | 3533 |
Missense in Polyphen | 63 | 99.805 | 0.63123 | 1205 | ||
Synonymous | 0.763 | 88 | 97.6 | 0.902 | 0.00000480 | 1018 |
Loss of Function | 3.65 | 5 | 24.5 | 0.204 | 0.00000126 | 320 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.000732 | 0.000732 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.000281 | 0.000278 |
Finnish | 0.00 | 0.00 |
European (Non-Finnish) | 0.0000531 | 0.0000353 |
Middle Eastern | 0.000281 | 0.000278 |
South Asian | 0.0000337 | 0.0000327 |
Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: RNA-binding protein that binds to misfolded non-coding RNAs, pre-5S rRNA, and several small cytoplasmic RNA molecules known as Y RNAs. May stabilize some of these RNAs and protect them from degradation. {ECO:0000269|PubMed:18056422}.;
- Pathway
- Systemic lupus erythematosus - Homo sapiens (human)
(Consensus)
Intolerance Scores
- loftool
- 0.264
- rvis_EVS
- -0.34
- rvis_percentile_EVS
- 30.56
Haploinsufficiency Scores
- pHI
- 0.0999
- hipred
- Y
- hipred_score
- 0.756
- ghis
- 0.641
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.978
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Trove2
- Phenotype
- integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); cellular phenotype; hematopoietic system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); renal/urinary system phenotype; immune system phenotype;
Gene ontology
- Biological process
- immune system development;transcription by RNA polymerase III;smoothened signaling pathway;response to UV;cilium assembly
- Cellular component
- nucleoplasm;cytosol;ribonucleoprotein complex
- Molecular function
- RNA binding;U2 snRNA binding;metal ion binding