YRDC

yrdC N6-threonylcarbamoyltransferase domain containing

Basic information

Region (hg38): 1:37802945-37808208

Links

ENSG00000196449NCBI:79693OMIM:612276HGNC:28905Uniprot:Q86U90AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

  • 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 ClinVar and linked to the YRDC gene.

  • 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.

EffectPLPVUSLBBSum
synonymous
24
clinvar
3
clinvar
27
missense
2
clinvar
59
clinvar
6
clinvar
67
nonsense
0
start loss
1
1
frameshift
1
clinvar
1
splice donor/acceptor (+/-2bp)
0
Total 3 0 60 30 3

Highest pathogenic variant AF is 0.00000362602

Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
YRDCprotein_codingprotein_codingENST00000373044 55242
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.002180.7701257350131257480.0000517
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.09841121150.9740.000006361725
Missense in Polyphen2536.2510.68963518
Synonymous-0.8615547.51.160.00000271626
Loss of Function0.95757.900.6333.35e-7107

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.00005780.0000578
Ashkenazi Jewish0.00009950.0000992
East Asian0.000.00
Finnish0.000.00
European (Non-Finnish)0.00006160.0000615
Middle Eastern0.000.00
South Asian0.00009800.0000980
Other0.000.00

dbNSFP

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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