DDX3Y

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

Basic information

Region (hg38): Y:12904108-12920478

Previous symbols: [ "DBY" ]

Links

ENSG00000067048NCBI:8653OMIM:400010HGNC:2699Uniprot:O15523AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

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)
  • not_provided (1 variants)
  • DDX3Y-related_disorder (1 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. These statistics are base on transcript: NM_000004660.5. Only rare variants are included in the table.

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.

EffectPLPVUSLBBSum
synonymous
2
clinvar
2
missense
0
nonsense
1
clinvar
1
start loss
0
frameshift
3
clinvar
3
splice donor/acceptor (+/-2bp)
1
clinvar
1
Total 0 5 0 2 0
Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
DDX3Yprotein_codingprotein_codingENST00000336079 1716372
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.9650.035000000.00
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense2.10531170.4530.00002014341
Missense in Polyphen541.0340.121851586
Synonymous0.9592633.00.7880.000004871247
Loss of Function2.99010.40.000.00000176456

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.000.00
Ashkenazi Jewish0.000.00
East Asian0.000.00
Finnish0.000.00
European (Non-Finnish)0.000.00
Middle Eastern0.000.00
South Asian0.000.00
Other0.000.00

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
essential_gene_gene_trap
gene_indispensability_pred
N
gene_indispensability_score
0.234

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Ddx3y
Phenotype

Gene ontology

Biological process
Cellular component
nucleus;cytosol;membrane
Molecular function
DNA binding;RNA binding;helicase activity;ATP binding