DDX60L

DExD/H-box 60 like, the group of Ski2 like RNA helicases

Basic information

Region (hg38): 4:168356734-168537786

Links

ENSG00000181381 ∙ NCBI:91351 ∙ OMIM:616725 ∙ HGNC:26429 ∙ Uniprot:Q5H9U9 ∙ 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 DDX60L gene.

• Inborn genetic diseases (72 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DDX60L 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				1		1
missense			68	4		72
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	68	5	0

Variants in DDX60L

This is a list of pathogenic ClinVar variants found in the DDX60L region.

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

Position	Type	Phenotype	Significance	ClinVar
4-168358152-C-T		not specified	Likely benign (Feb 06, 2023)
4-168358158-G-T		not specified	Uncertain significance (Mar 29, 2022)
4-168358221-T-C		not specified	Likely benign (Sep 16, 2021)
4-168358274-T-A		not specified	Likely benign (Aug 19, 2023)
4-168361164-T-C		not specified	Uncertain significance (Mar 20, 2023)
4-168361209-A-G		not specified	Uncertain significance (Jun 12, 2023)
4-168371670-C-T		not specified	Uncertain significance (Aug 15, 2023)
4-168371681-A-G		not specified	Uncertain significance (Mar 31, 2023)
4-168371732-G-C		not specified	Uncertain significance (Nov 14, 2023)
4-168371742-C-T		not specified	Likely benign (Jan 03, 2024)
4-168371745-C-T		not specified	Uncertain significance (Apr 28, 2023)
4-168371760-T-A		not specified	Uncertain significance (Mar 14, 2023)
4-168373699-A-T		not specified	Uncertain significance (May 11, 2022)
4-168373776-G-T		not specified	Uncertain significance (Feb 27, 2024)
4-168375436-A-G		not specified	Uncertain significance (Jan 19, 2024)
4-168375485-A-C		not specified	Uncertain significance (Feb 26, 2024)
4-168375509-G-C		not specified	Uncertain significance (Jun 03, 2022)
4-168378413-C-T		not specified	Uncertain significance (Aug 22, 2023)
4-168378475-C-A		not specified	Uncertain significance (Jan 26, 2022)
4-168379377-T-G		not specified	Uncertain significance (Jun 13, 2022)
4-168379438-C-T		not specified	Uncertain significance (May 05, 2023)
4-168379446-T-C		not specified	Uncertain significance (Aug 12, 2021)
4-168384632-G-A		not specified	Uncertain significance (Mar 08, 2024)
4-168384640-C-T		not specified	Uncertain significance (May 31, 2023)
4-168384685-A-G		not specified	Uncertain significance (Oct 29, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DDX60L	protein_coding	protein_coding	ENST00000260184	37	181052

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.07e-38	0.000997	125322	2	424	125748	0.00170

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.114	776	785	0.989	0.0000393	11171
Missense in Polyphen		205	217.27	0.94351		3078
Synonymous	-0.434	302	293	1.03	0.0000157	3025
Loss of Function	1.50	67	81.7	0.820	0.00000413	1194

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00792	0.00776
Ashkenazi Jewish	0.00845	0.00837
East Asian	0.000390	0.000381
Finnish	0.0000477	0.0000462
European (Non-Finnish)	0.00129	0.00127
Middle Eastern	0.000390	0.000381
South Asian	0.000745	0.000719
Other	0.00299	0.00294

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0727

Intolerance Scores

• rvis_EVS: 2.62
• rvis_percentile_EVS: 98.78

Haploinsufficiency Scores

• pHI: 0.0716
• hipred: N
• hipred_score: 0.112
• ghis: 0.422

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.129

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	High	High	High
Primary Immunodeficiency	High	High	High
Cancer	High	High	High

Gene ontology

• Molecular function: RNA binding;helicase activity;ATP binding