DHX40

DEAH-box helicase 40, the group of NTC associated proteins|DEAH-box helicases

Basic information

Region (hg38): 17:59565558-59608345

Previous symbols: [ "DDX40" ]

Links

ENSG00000108406 ∙ NCBI:79665 ∙ OMIM:607570 ∙ HGNC:18018 ∙ Uniprot:Q8IX18 ∙ 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 DHX40 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DHX40 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					1	1
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	0	1

Variants in DHX40

This is a list of pathogenic ClinVar variants found in the DHX40 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-59565703-C-A		not specified	Uncertain significance (Aug 05, 2024)
17-59566632-A-G		not specified	Uncertain significance (May 06, 2024)
17-59566786-A-G		not specified	Uncertain significance (Sep 16, 2021)
17-59566786-A-T		not specified	Uncertain significance (Nov 09, 2024)
17-59570536-T-C		not specified	Uncertain significance (Nov 17, 2022)
17-59570603-G-A		not specified	Uncertain significance (Aug 02, 2021)
17-59570615-G-C		not specified	Uncertain significance (Apr 26, 2024)
17-59573206-G-A		not specified	Uncertain significance (Oct 20, 2024)
17-59573759-T-G		not specified	Uncertain significance (Jan 31, 2022)
17-59573778-G-C		not specified	Uncertain significance (Jan 03, 2024)
17-59573809-G-A		not specified	Uncertain significance (Jul 27, 2022)
17-59573835-A-G			Benign (Mar 29, 2018)
17-59573839-G-A		not specified	Uncertain significance (Jan 30, 2024)
17-59573884-C-T		not specified	Uncertain significance (Oct 05, 2021)
17-59573936-G-A		not specified	Uncertain significance (Jun 28, 2022)
17-59575421-C-T		not specified	Uncertain significance (Aug 13, 2021)
17-59575424-C-T		not specified	Uncertain significance (Sep 04, 2024)
17-59577319-A-G		not specified	Uncertain significance (Jun 10, 2024)
17-59579545-G-A		not specified	Uncertain significance (Aug 21, 2024)
17-59587919-G-C		not specified	Uncertain significance (Aug 04, 2024)
17-59587952-A-G		not specified	Uncertain significance (Sep 06, 2022)
17-59587982-C-T		not specified	Uncertain significance (Mar 31, 2024)
17-59598818-C-G		not specified	Uncertain significance (Mar 11, 2022)
17-59598833-T-A		not specified	Uncertain significance (Dec 07, 2021)
17-59599377-G-A		not specified	Uncertain significance (Dec 12, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DHX40	protein_coding	protein_coding	ENST00000251241	18	42821

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.756	0.244	125726	1	19	125746	0.0000795

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.02	209	373	0.560	0.0000189	5092
Missense in Polyphen		48	120.88	0.39709		1644
Synonymous	0.624	116	125	0.929	0.00000623	1449
Loss of Function	4.67	8	39.8	0.201	0.00000228	544

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000341	0.000340
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000548	0.0000544
Finnish	0.000221	0.000185
European (Non-Finnish)	0.0000443	0.0000439
Middle Eastern	0.0000548	0.0000544
South Asian	0.0000333	0.0000327
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Probable ATP-dependent RNA helicase. {ECO:0000250}.
• Pathway: miR-targeted genes in epithelium - TarBase;miR-targeted genes in lymphocytes - TarBase;miR-targeted genes in muscle cell - TarBase;miR-targeted genes in squamous cell - TarBase (Consensus)

Recessive Scores

• pRec: 0.133

Intolerance Scores

• loftool: 0.558
• rvis_EVS: -0.8
• rvis_percentile_EVS: 12.24

Haploinsufficiency Scores

• pHI: 0.294
• hipred: Y
• hipred_score: 0.688
• ghis: 0.655

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.840

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Dhx40
• Phenotype: cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); skeleton phenotype; vision/eye phenotype; homeostasis/metabolism phenotype

Gene ontology

• Biological process: mRNA splicing, via spliceosome
• Molecular function: RNA binding;ATP binding;ATP-dependent 3'-5' RNA helicase activity