YRDC

protein-coding

yrdC N6-threonylcarbamoyltransferase domain containing

Gene summary

Enables L-threonylcarbamoyladenylate synthase activity. Involved in tRNA threonylcarbamoyladenosine modification. Acts upstream of or within negative regulation of transport. Is active in mitochondrion. Implicated in Galloway-Mowat syndrome. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_024640.4

Inheritance

ClinVar variants

P:4U:69B:36

Top phenotype

Galloway-Mowat syndrome 10

gnomAD constraint

pLI —, LoF o/e 0.63

Max pathogenic AF

—

Genomic locus

chr1:37,802,945-37,808,208

External References & Databases

Ensembl (ENSG00000196449)

Transcript & Mutation Effects

hg38 • Region Span ~5.3 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

Galloway-Mowat syndrome 10STRONG

Inheritance Pattern: AR

Disease ID:MONDO:0030476

Submitter: G2P

Galloway-Mowat syndrome 10STRONG

Inheritance Pattern: AR

Disease ID:MONDO:0030476

Submitter: Labcorp Genetics (formerly Invitae)

Galloway-Mowat syndrome 10STRONG

Inheritance Pattern: AR

Disease ID:MONDO:0030476

Submitter: PanelApp Australia

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to YRDC variants in ClinVar

4 Conditions Cataloged

not specifiedTotal: 67

not providedTotal: 40

YRDC-related disorderTotal: 17

Galloway-Mowat syndrome 10Total: 5

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_024640.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			1 clinvar	29 clinvar	1 clinvar	31
missense	2 clinvar	1 clinvar	66 clinvar	6 clinvar		75
nonsense			1 clinvar			1
start loss			1 clinvar			1
frameshift	1 clinvar					1
splice donor/acceptor (+/-2bp)						0
Total	3	1	69	35	1	109

Highest pathogenic variant AF is 0.0000036260196

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 6 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_024640.4	RefSeq	NP_078916.3	5	MANE Select
ENST00000373044.3	Ensembl	ENSP00000362135.2	5	MANE Select
ENST00000882854.1	Ensembl	ENSP00000552913.1	5	Standard
ENST00000882854.2	Ensembl	ENSP00000552913.1	5	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

regulation of translational fidelity
negative regulation of transport

Molecular Function

tRNA binding
double-stranded RNA binding
nucleotidyltransferase activity

Cellular Component

cytoplasm
mitochondrion
membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000373044
Coding exons: 5
Length: 5242
Individuals with no LoFs: 125735
Homozygous LoFs: 0
Heterozygous LoFs: 13
Defined: 125748
p: 0.0000517

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.0984	112	115	0.974	0.00000636	1725
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000058	0.000058	rare
Ashkenazi Jewish	0.000099	0.000099	rare
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.000062	0.000062	rare
South Asian	0.000098	0.000098	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May regulate the activity of some transporters. {ECO:0000250}.;

Recessive Scores

pRec: 0.170

Essentials

Essential (CRISPR): E
Essential (CRISPR2): E
Essential (gene trap): E
Indispensability pred.: E
Indispensability score: 0.761

Gene Damage Prediction

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