DDX3Y

DEAD-box helicase 3 Y-linked, the group of DEAD-box helicases|Minor histocompatibility antigens

Basic information

Region (hg38): Y:12904107-12920478

Previous symbols: [ "DBY" ]

Links

ENSG00000067048 ∙ NCBI:8653 ∙ OMIM:400010 ∙ HGNC:2699 ∙ Uniprot:O15523 ∙ 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 DDX3Y gene.

• Non-obstructive azoospermia (4 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DDX3Y 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						0
nonsense		1				1
start loss						0
frameshift		2				2
inframe indel						0
splice donor/acceptor (+/-2bp)		1				1
splice region						0
non coding						0
Total	0	4	0	0	0

Variants in DDX3Y

This is a list of pathogenic ClinVar variants found in the DDX3Y region.

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

Position	Type	Phenotype	Significance	ClinVar
Y-12912872-C-CG		Non-obstructive azoospermia	Likely pathogenic (Jan 12, 2023)
Y-12915726-C-T		DDX3Y-related disorder	Likely benign (Jun 07, 2019)
Y-12915947-CTG-C		Non-obstructive azoospermia	Likely pathogenic (Jan 12, 2023)
Y-12915989-A-AT		Non-obstructive azoospermia	Likely pathogenic (Jan 12, 2023)
Y-12916632-TG-T		Non-obstructive azoospermia	Likely pathogenic (Jan 12, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DDX3Y	protein_coding	protein_coding	ENST00000336079	17	16372

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.965	0.0350	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.10	53	117	0.453	0.0000201	4341
Missense in Polyphen		5	41.034	0.12185		1586
Synonymous	0.959	26	33.0	0.788	0.00000487	1247
Loss of Function	2.99	0	10.4	0.00	0.00000176	456

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

• Function: FUNCTION: Probable ATP-dependent RNA helicase. May play a role in spermatogenesis.
• Pathway: RIG-I-like Receptor Signaling (Consensus)

Haploinsufficiency Scores

• pHI: 0.409
• hipred: N
• hipred_score: 0.434
• ghis: 0.484

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.234

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ddx3y

Gene ontology

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