YRDC
Basic information
Region (hg38): 1:37802945-37808208
Links
Phenotypes
GenCC
Source:
- Galloway-Mowat syndrome 10 (Strong), mode of inheritance: AR
- Galloway-Mowat syndrome 10 (Strong), mode of inheritance: AR
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (59 variants)
- not_provided (33 variants)
- YRDC-related_disorder (16 variants)
- Galloway-Mowat_syndrome_10 (4 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the YRDC gene is commonly pathogenic or not. These statistics are base on transcript: NM_000024640.4. Only rare variants are included in the table.
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.
Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
---|---|---|---|---|---|---|
synonymous | 24 | 27 | ||||
missense | 59 | 67 | ||||
nonsense | 0 | |||||
start loss | 1 | 1 | ||||
frameshift | 1 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
Total | 3 | 0 | 60 | 30 | 3 |
Highest pathogenic variant AF is 0.00000362602
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
YRDC | protein_coding | protein_coding | ENST00000373044 | 5 | 5242 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.00218 | 0.770 | 125735 | 0 | 13 | 125748 | 0.0000517 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 0.0984 | 112 | 115 | 0.974 | 0.00000636 | 1725 |
Missense in Polyphen | 25 | 36.251 | 0.68963 | 518 | ||
Synonymous | -0.861 | 55 | 47.5 | 1.16 | 0.00000271 | 626 |
Loss of Function | 0.957 | 5 | 7.90 | 0.633 | 3.35e-7 | 107 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.0000578 | 0.0000578 |
Ashkenazi Jewish | 0.0000995 | 0.0000992 |
East Asian | 0.00 | 0.00 |
Finnish | 0.00 | 0.00 |
European (Non-Finnish) | 0.0000616 | 0.0000615 |
Middle Eastern | 0.00 | 0.00 |
South Asian | 0.0000980 | 0.0000980 |
Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: May regulate the activity of some transporters. {ECO:0000250}.;
Recessive Scores
- pRec
- 0.170
Haploinsufficiency Scores
- pHI
- 0.464
- hipred
- N
- hipred_score
- 0.231
- ghis
- 0.600
Essentials
- essential_gene_CRISPR
- E
- essential_gene_CRISPR2
- E
- essential_gene_gene_trap
- E
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.761
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Yrdc
- Phenotype
Gene ontology
- Biological process
- regulation of translational fidelity;negative regulation of transport
- Cellular component
- cytoplasm;mitochondrion;membrane
- Molecular function
- tRNA binding;double-stranded RNA binding;nucleotidyltransferase activity