DDX25

DEAD-box helicase 25, the group of DEAD-box helicases

Basic information

Region (hg38): 11:125903348-125943702

Links

ENSG00000109832 ∙ NCBI:29118 ∙ OMIM:607663 ∙ HGNC:18698 ∙ Uniprot:Q9UHL0 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

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

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the DDX25 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DDX25 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	3
missense			30			30
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1	1	2
non coding					20	20
Total	0	0	30	0	23

Variants in DDX25

This is a list of pathogenic ClinVar variants found in the DDX25 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-125904062-G-C			Benign (Nov 11, 2018)
11-125904156-C-T			Benign (Nov 11, 2018)
11-125904191-G-T			Benign (Nov 10, 2018)
11-125904265-TCGCCCCGCTCTCTGCCCTC-T			Benign (Nov 11, 2018)
11-125904528-T-C		not specified	Uncertain significance (Jun 05, 2023)
11-125904535-G-C		not specified	Uncertain significance (May 16, 2023)
11-125904544-C-G		not specified	Uncertain significance (Mar 31, 2023)
11-125904561-G-C		not specified	Uncertain significance (Apr 06, 2024)
11-125904566-C-T		not specified	Uncertain significance (Aug 14, 2023)
11-125905215-T-C		not specified	Uncertain significance (Sep 26, 2024)
11-125905259-T-A		not specified	Uncertain significance (Dec 20, 2023)
11-125905559-C-T		not specified	Uncertain significance (Nov 09, 2023)
11-125906170-C-G		not specified	Uncertain significance (Apr 17, 2023)
11-125906364-G-C			Benign (Nov 11, 2018)
11-125906472-C-T			Benign (Nov 10, 2018)
11-125908055-G-T			Benign (Jun 19, 2021)
11-125908261-T-C		not specified	Uncertain significance (Dec 28, 2023)
11-125908324-T-C			Benign (Jun 19, 2021)
11-125908410-C-T			Benign (Apr 19, 2018)
11-125908461-G-C		not specified	Uncertain significance (Feb 22, 2023)
11-125908470-A-C		not specified	Uncertain significance (Nov 12, 2024)
11-125908471-A-G		not specified	Uncertain significance (Apr 07, 2023)
11-125908486-T-G		not specified	Uncertain significance (Jan 03, 2024)
11-125908498-C-T		not specified	Uncertain significance (Oct 18, 2021)
11-125908556-T-A			Benign (Nov 10, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DDX25	protein_coding	protein_coding	ENST00000263576	12	19888

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.81e-18	0.00650	124608	0	44	124652	0.000177

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.21	211	267	0.791	0.0000149	3173
Missense in Polyphen		81	102.39	0.79107		1185
Synonymous	0.546	88	94.8	0.929	0.00000517	900
Loss of Function	0.214	28	29.3	0.957	0.00000187	308

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000404	0.000394
Ashkenazi Jewish	0.000100	0.0000994
East Asian	0.000167	0.000167
Finnish	0.000373	0.000371
European (Non-Finnish)	0.000136	0.000133
Middle Eastern	0.000167	0.000167
South Asian	0.000136	0.000131
Other	0.000331	0.000330

dbNSFP

Source: dbNSFP

• Function: FUNCTION: ATP-dependent RNA helicase. Required for mRNA export and translation regulation during spermatid development (By similarity). {ECO:0000250, ECO:0000269|PubMed:10608860}.

Recessive Scores

• pRec: 0.106

Intolerance Scores

• loftool: 0.735
• rvis_EVS: -0.45
• rvis_percentile_EVS: 24.19

Haploinsufficiency Scores

• pHI: 0.569
• hipred: N
• hipred_score: 0.411
• ghis: 0.591

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.557

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ddx25
• Phenotype: cellular phenotype; endocrine/exocrine gland phenotype; reproductive system phenotype

Gene ontology

• Biological process: mRNA export from nucleus;regulation of translation;multicellular organism development;spermatid development
• Cellular component: nucleus;cytoplasm;chromatoid body
• Molecular function: RNA binding;ATP-dependent RNA helicase activity;ATP binding