DDX53

DEAD-box helicase 53, the group of DEAD-box helicases

Basic information

Region (hg38): X:22999959-23003589

Links

ENSG00000184735 ∙ NCBI:168400 ∙ OMIM:301079 ∙ HGNC:20083 ∙ Uniprot:Q86TM3 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• male infertility with azoospermia or oligozoospermia due to single gene mutation (Limited), mode of inheritance: XL

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the DDX53 gene.

• Inborn genetic diseases (20 variants)
• not provided (14 variants)
• not specified (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DDX53 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				3	2	5
missense			21	3	3	27
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	21	6	5

Variants in DDX53

This is a list of pathogenic ClinVar variants found in the DDX53 region.

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

Position	Type	Phenotype	Significance	ClinVar
X-23000070-G-A		DDX53-related disorder	Benign/Likely benign (Dec 01, 2022)
X-23000081-G-A		Nephrotic syndrome	Uncertain significance (Nov 10, 2017)
X-23000137-G-A		not specified	Conflicting classifications of pathogenicity (Apr 12, 2023)
X-23000153-G-C		not specified	Uncertain significance (Aug 13, 2021)
X-23000170-A-G		DDX53-related disorder	Benign (Dec 31, 2019)
X-23000242-T-C		DDX53-related disorder	Benign (Nov 25, 2019)
X-23000264-A-C			Likely benign (Apr 01, 2023)
X-23000274-G-C		DDX53-related disorder • not specified	Conflicting classifications of pathogenicity (Jul 05, 2023)
X-23000316-G-T			Uncertain significance (Oct 24, 2022)
X-23000317-G-C		not specified	Uncertain significance (Sep 13, 2023)
X-23000344-T-C		not specified	Uncertain significance (Dec 26, 2023)
X-23000372-C-T		DDX53-related disorder	Benign (Nov 25, 2019)
X-23000376-G-T		not specified • DDX53-related disorder	Benign/Likely benign (Feb 28, 2022)
X-23000422-A-C		not specified	Uncertain significance (Jul 13, 2021)
X-23000457-A-G		DDX53-related disorder • not specified	Likely benign (Jul 01, 2022)
X-23000545-G-A			Uncertain significance (Oct 21, 2016)
X-23000547-G-A		DDX53-related disorder	Likely benign (Jul 30, 2023)
X-23000621-G-A		not specified	Uncertain significance (Jan 23, 2024)
X-23000628-A-G		not specified	Uncertain significance (Dec 06, 2022)
X-23000697-C-T		DDX53-related disorder	Likely benign (Dec 16, 2019)
X-23000706-C-T		not specified	Uncertain significance (Mar 07, 2023)
X-23000844-A-G		not specified	Uncertain significance (Mar 24, 2023)
X-23000869-G-A		not specified	Uncertain significance (Dec 12, 2016)
X-23000870-G-A			Likely benign (Sep 01, 2022)
X-23001055-G-A		not specified	Uncertain significance (Dec 21, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DDX53	protein_coding	protein_coding	ENST00000327968	1	2118

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.662	0.317	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.00519	240	240	0.999	0.0000180	4175
Missense in Polyphen		63	79.301	0.79444		1486
Synonymous	-1.07	100	87.3	1.15	0.00000705	1217
Loss of Function	1.74	0	3.52	0.00	2.23e-7	61

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.103

Intolerance Scores

• loftool: 0.481
• rvis_EVS: 0.42
• rvis_percentile_EVS: 77.23

Haploinsufficiency Scores

• pHI: 0.0199
• hipred: N
• hipred_score: 0.293

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.475

Gene Damage Prediction

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

Gene ontology

• Cellular component: nucleus
• Molecular function: RNA binding;helicase activity;ATP binding