DHX15

DEAH-box helicase 15, the group of Spliceosomal A complex|DEAH-box helicases|SSU processome|Spliceosomal B complex|U11/U12 di-snRNP

Basic information

Region (hg38): 4:24517441-24584554

Previous symbols: [ "DDX15" ]

Links

ENSG00000109606 ∙ NCBI:1665 ∙ OMIM:603403 ∙ HGNC:2738 ∙ Uniprot:O43143 ∙ 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 DHX15 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DHX15 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				2		2
missense			20			20
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	20	2	0

Variants in DHX15

This is a list of pathogenic ClinVar variants found in the DHX15 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-24527962-T-C		not specified	Uncertain significance (Aug 25, 2024)
4-24527967-C-T		not specified	Uncertain significance (Feb 26, 2025)
4-24527982-T-C		not specified	Uncertain significance (Dec 18, 2023)
4-24532922-G-A		not specified	Uncertain significance (Jun 04, 2024)
4-24532989-T-C		not specified	Uncertain significance (Feb 02, 2024)
4-24540170-A-G		not specified	Uncertain significance (Dec 14, 2023)
4-24540945-T-C		not specified	Uncertain significance (Aug 21, 2024)
4-24542948-T-C		8 conditions	Uncertain significance (-)
4-24548908-G-A		not specified	Uncertain significance (Apr 06, 2023)
4-24554806-T-C			Likely benign (Jun 01, 2020)
4-24556385-G-A		not specified	Uncertain significance (Jan 23, 2023)
4-24570805-G-C		not specified	Uncertain significance (Aug 17, 2022)
4-24576396-G-A			Likely benign (Aug 01, 2022)
4-24576424-G-A		not specified	Uncertain significance (May 23, 2023)
4-24576436-T-C		not specified	Uncertain significance (Nov 01, 2022)
4-24576446-G-A		not specified	Uncertain significance (Apr 18, 2023)
4-24576448-G-A		not specified	Uncertain significance (Mar 28, 2023)
4-24576464-G-A		not specified	Uncertain significance (Jun 02, 2023)
4-24576475-G-A		not specified	Uncertain significance (Jun 17, 2024)
4-24576502-G-C		not specified	Uncertain significance (Jan 10, 2025)
4-24576508-T-C		not specified	Uncertain significance (Nov 09, 2024)
4-24576619-C-T		not specified	Uncertain significance (Mar 18, 2024)
4-24576625-C-T		not specified	Uncertain significance (May 05, 2023)
4-24584329-G-A		not specified	Uncertain significance (Sep 04, 2024)
4-24584345-T-G		not specified	Uncertain significance (Feb 18, 2025)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DHX15	protein_coding	protein_coding	ENST00000336812	14	67110

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	4.08e-7	125717	0	2	125719	0.00000795

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	5.63	115	452	0.255	0.0000247	5195
Missense in Polyphen		7	190.01	0.036841		2214
Synonymous	-0.446	156	149	1.05	0.00000753	1541
Loss of Function	6.10	1	45.3	0.0221	0.00000305	489

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)	0.0000177	0.0000176
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Pre-mRNA processing factor involved in disassembly of spliceosomes after the release of mature mRNA. In cooperation with TFIP11 seem to be involved in the transition of the U2, U5 and U6 snRNP-containing IL complex to the snRNP-free IS complex leading to efficient debranching and turnover of excised introns. {ECO:0000269|PubMed:19103666}.
• Pathway: Spliceosome - Homo sapiens (human);miR-targeted genes in epithelium - TarBase;miR-targeted genes in lymphocytes - TarBase;miR-targeted genes in muscle cell - TarBase;mRNA Processing;Metabolism of RNA;mRNA Splicing - Major Pathway;mRNA Splicing;Processing of Capped Intron-Containing Pre-mRNA (Consensus)

Recessive Scores

• pRec: 0.450

Intolerance Scores

• rvis_EVS: -0.82
• rvis_percentile_EVS: 11.68

Haploinsufficiency Scores

• pHI: 0.984
• hipred: Y
• hipred_score: 0.783
• ghis: 0.730

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.876

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Dhx15

Gene ontology

• Biological process: mRNA splicing, via spliceosome;mRNA processing;RNA splicing;response to toxic substance;response to alkaloid
• Cellular component: nucleus;nucleoplasm;U12-type spliceosomal complex;nucleolus;nuclear speck;U2-type post-mRNA release spliceosomal complex
• Molecular function: RNA binding;RNA helicase activity;double-stranded RNA binding;protein binding;ATP binding;ATP-dependent 3'-5' RNA helicase activity