DUS4L

dihydrouridine synthase 4 like

Basic information

Region (hg38): 7:107563483-107578523

Links

ENSG00000105865 ∙ NCBI:11062 ∙ ∙ HGNC:21517 ∙ Uniprot:O95620 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the DUS4L gene.

• COG5-congenital disorder of glycosylation (22 variants)
• Inborn genetic diseases (6 variants)
• not specified (4 variants)
• not provided (3 variants)
• Congenital disorder of glycosylation (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DUS4L 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						0
missense			6			6
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding		2	13	7	1	23
Total	0	2	19	7	1

Variants in DUS4L

This is a list of pathogenic ClinVar variants found in the DUS4L region.

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

Position	Type	Phenotype	Significance	ClinVar
7-107563543-AT-A			Likely benign (Feb 13, 2020)
7-107563544-T-G			Benign (Feb 13, 2020)
7-107563544-TG-T			Benign (Oct 29, 2019)
7-107563544-TGG-T			Benign (Oct 12, 2019)
7-107563544-TGGG-T			Benign (Apr 12, 2020)
7-107563544-T-TG			Likely benign (Feb 14, 2020)
7-107563545-G-GGC			Likely benign (Feb 13, 2020)
7-107563546-G-GC			Benign (Oct 29, 2019)
7-107563788-AC-A		COG5-congenital disorder of glycosylation	Benign (Aug 03, 2023)
7-107563791-C-A		COG5-congenital disorder of glycosylation	Likely benign (Dec 18, 2023)
7-107563793-G-C		COG5-congenital disorder of glycosylation	Likely benign (Feb 02, 2021)
7-107563795-C-T		COG5-congenital disorder of glycosylation	Likely benign (Jun 29, 2023)
7-107563800-T-C		COG5-congenital disorder of glycosylation	Uncertain significance (Jan 12, 2018)
7-107563804-G-A		COG5-congenital disorder of glycosylation	Uncertain significance (Jul 21, 2022)
7-107563815-G-T		COG5-congenital disorder of glycosylation	Uncertain significance (Sep 28, 2022)
7-107563815-GT-G		COG5-congenital disorder of glycosylation	Conflicting classifications of pathogenicity (Dec 02, 2021)
7-107563827-T-C		COG5-congenital disorder of glycosylation	Uncertain significance (Feb 08, 2019)
7-107563829-G-C		COG5-congenital disorder of glycosylation	Uncertain significance (Aug 16, 2022)
7-107563830-C-G		COG5-congenital disorder of glycosylation	Uncertain significance (Oct 17, 2022)
7-107563837-C-T		COG5-congenital disorder of glycosylation	Likely benign (Oct 30, 2022)
7-107563838-G-A		COG5-congenital disorder of glycosylation	Uncertain significance (Jul 08, 2022)
7-107563846-G-A		COG5-congenital disorder of glycosylation	Likely benign (Sep 25, 2023)
7-107563847-C-A		COG5-congenital disorder of glycosylation • Inborn genetic diseases • COG5-related disorder	Conflicting classifications of pathogenicity (Feb 01, 2024)
7-107563850-C-T		COG5-congenital disorder of glycosylation	Uncertain significance (Sep 01, 2021)
7-107563851-G-A		COG5-congenital disorder of glycosylation	Pathogenic (Jul 19, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DUS4L	protein_coding	protein_coding	ENST00000265720	6	14978

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000318	0.812	125642	0	104	125746	0.000414

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.750	144	172	0.839	0.00000820	2094
Missense in Polyphen		54	66.926	0.80687		824
Synonymous	1.61	40	55.2	0.725	0.00000292	578
Loss of Function	1.26	9	14.1	0.638	6.58e-7	187

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000668	0.000665
Ashkenazi Jewish	0.000101	0.0000992
East Asian	0.000327	0.000326
Finnish	0.0000463	0.0000462
European (Non-Finnish)	0.000462	0.000457
Middle Eastern	0.000327	0.000326
South Asian	0.000853	0.000850
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Catalyzes the synthesis of dihydrouridine, a modified base found in the D-loop of most tRNAs. {ECO:0000250}.

Recessive Scores

• pRec: 0.179

Intolerance Scores

• loftool: 0.847
• rvis_EVS: 0.02
• rvis_percentile_EVS: 55.22

Haploinsufficiency Scores

• pHI: 0.507
• hipred: N
• hipred_score: 0.292
• ghis: 0.609

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.780

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Dus4l

Gene ontology

• Biological process: tRNA dihydrouridine synthesis;oxidation-reduction process
• Molecular function: tRNA dihydrouridine synthase activity;flavin adenine dinucleotide binding