YRDC

yrdC N6-threonylcarbamoyltransferase domain containing

Basic information

Region (hg38): 1:37802945-37808208

Links

ENSG00000196449 ∙ NCBI:79693 ∙ OMIM:612276 ∙ HGNC:28905 ∙ Uniprot:Q86U90 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• 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.

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.

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				21	2	23
missense			25	3		28
nonsense						0
start loss			1			1
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding				3	1	4
Total	0	0	26	27	3

Variants in YRDC

This is a list of pathogenic ClinVar variants found in the YRDC region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
1-37803930-G-A			Likely benign (May 15, 2022)
1-37803937-C-T		YRDC-related disorder	Likely benign (Apr 01, 2022)
1-37803942-G-A		not specified	Uncertain significance (Oct 13, 2023)
1-37803957-C-T		not specified	Uncertain significance (Jul 14, 2021)
1-37803958-G-A			Likely benign (Jun 12, 2022)
1-37803964-C-A		not specified	Uncertain significance (Oct 08, 2024)
1-37803968-TGGA-T		Galloway-Mowat syndrome 10	Pathogenic (Nov 10, 2021)
1-37804330-C-T			Conflicting classifications of pathogenicity (Sep 27, 2023)
1-37804331-G-A			Likely benign (Jan 22, 2024)
1-37804333-G-A		not specified	Conflicting classifications of pathogenicity (Sep 19, 2023)
1-37804340-C-A		not specified	Uncertain significance (Feb 01, 2023)
1-37804340-C-T		YRDC-related disorder	Likely benign (Jan 31, 2020)
1-37804344-TCAAC-T		Galloway-Mowat syndrome 10	Pathogenic (Nov 10, 2021)
1-37804373-G-A		YRDC-related disorder	Benign (Dec 22, 2023)
1-37804393-T-G		not specified	Uncertain significance (May 09, 2023)
1-37804405-C-T		not specified	Uncertain significance (Nov 17, 2022)
1-37804407-A-G		Galloway-Mowat syndrome 10	Pathogenic (Nov 10, 2021)
1-37804411-C-T		not specified	Uncertain significance (Jun 07, 2024)
1-37806844-T-G			Likely benign (Nov 13, 2023)
1-37806859-C-T		not specified	Uncertain significance (Oct 16, 2024)
1-37806885-C-G		not specified	Uncertain significance (Nov 15, 2024)
1-37806891-T-C		not specified	Uncertain significance (Oct 28, 2023)
1-37806911-C-A		YRDC-related disorder	Likely benign (Apr 13, 2022)
1-37806912-G-A		not specified	Uncertain significance (Jun 29, 2022)
1-37806988-G-A			Benign (Jan 30, 2024)

GnomAD

Source: gnomAD

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: 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

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Yrdc

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