DHX30

DExH-box helicase 30, the group of DEAH-box helicases|MicroRNA protein coding host genes

Basic information

Region (hg38): 3:47802909-47850195

Previous symbols: [ "DDX30" ]

Links

ENSG00000132153 ∙ NCBI:22907 ∙ OMIM:616423 ∙ HGNC:16716 ∙ Uniprot:Q7L2E3 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• neurodevelopmental disorder with severe motor impairment and absent language (Strong), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Neurodevelopmental disorder with variable motor and language impairment	AD	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Craniofacial; Musculoskeletal; Neurologic	28327206; 29100085

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the DHX30 gene.

• Neurodevelopmental disorder with severe motor impairment and absent language (4 variants)
• 7 conditions (1 variants)
• 8 conditions (1 variants)
• Autism, susceptiblity to (1 variants)
• not provided (1 variants)
• Autism;Abnormal cerebral white matter morphology;Intellectual disability (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DHX30 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				29	2	31
missense	4	3	94	15	1	117
nonsense		1	3			4
start loss						0
frameshift			4			4
inframe indel			1			1
splice donor/acceptor (+/-2bp)	1	1				2
splice region			5	3	1	9
non coding			1	1		2
Total	5	5	103	45	3

Variants in DHX30

This is a list of pathogenic ClinVar variants found in the DHX30 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-47810708-A-T			Uncertain significance (Feb 04, 2023)
3-47818066-C-T		Neurodevelopmental disorder with severe motor impairment and absent language	Uncertain significance (Sep 23, 2021)
3-47818068-C-G			Likely benign (Oct 01, 2023)
3-47818093-A-G			Uncertain significance (Jul 01, 2023)
3-47818108-A-G			Uncertain significance (Jul 16, 2024)
3-47827467-C-T		Neurodevelopmental disorder with severe motor impairment and absent language	Conflicting classifications of pathogenicity (Oct 04, 2020)
3-47829021-C-T			Uncertain significance (Jan 13, 2023)
3-47829026-A-G			Uncertain significance (Sep 12, 2023)
3-47829038-C-A		Neurodevelopmental disorder with severe motor impairment and absent language	Uncertain significance (Jan 07, 2021)
3-47829056-C-T			Likely benign (Jul 01, 2024)
3-47840943-C-G		Inborn genetic diseases	Likely benign (Aug 28, 2023)
3-47840951-CT-GA		not specified	Uncertain significance (Oct 18, 2023)
3-47840953-C-A		Inborn genetic diseases	Uncertain significance (Feb 16, 2023)
3-47840960-C-T			Likely benign (May 01, 2023)
3-47840961-G-T			Uncertain significance (Jan 06, 2023)
3-47840989-T-C		Inborn genetic diseases	Uncertain significance (May 02, 2024)
3-47841000-TC-T			Uncertain significance (Jun 05, 2023)
3-47841013-T-G		Inborn genetic diseases	Uncertain significance (Mar 28, 2023)
3-47841019-C-G		Neurodevelopmental disorder with severe motor impairment and absent language • Inborn genetic diseases • DHX30-related disorder	Conflicting classifications of pathogenicity (Mar 29, 2023)
3-47841027-A-G		DHX30-related disorder	Benign (Mar 01, 2019)
3-47841031-G-A		not specified	Uncertain significance (Sep 08, 2023)
3-47841046-G-T			Uncertain significance (May 24, 2022)
3-47841070-G-A		Inborn genetic diseases	Likely benign (Aug 04, 2022)
3-47841087-G-A		Neurodevelopmental disorder with severe motor impairment and absent language	Uncertain significance (Jan 17, 2022)
3-47841114-A-G		Inborn genetic diseases	Likely benign (Jun 30, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DHX30	protein_coding	protein_coding	ENST00000445061	20	47287

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	5.71e-8	125731	0	17	125748	0.0000676

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	5.30	352	764	0.461	0.0000522	7676
Missense in Polyphen		33	198.72	0.16606		2009
Synonymous	-1.38	348	317	1.10	0.0000201	2555
Loss of Function	6.62	2	55.0	0.0364	0.00000307	576

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000738	0.000738
Ashkenazi Jewish	0.000202	0.000198
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000264	0.0000264
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: RNA-dependent helicase (PubMed:29100085). Plays an important role in the assembly of the mitochondrial large ribosomal subunit (PubMed:25683715, PubMed:29100085). Required for optimal function of the zinc-finger antiviral protein ZC3HAV1 (By similarity). Associates with mitochondrial DNA (PubMed:18063578). Involved in nervous system development and differentiation through its involvement in the up-regulation of a number of genes which are required for neurogenesis, including GSC, NCAM1, neurogenin, and NEUROD (By similarity). {ECO:0000250|UniProtKB:Q5BJS0, ECO:0000250|UniProtKB:Q99PU8, ECO:0000269|PubMed:18063578, ECO:0000269|PubMed:25683715, ECO:0000269|PubMed:29100085}.
• Disease: DISEASE: Neurodevelopmental disorder with severe motor impairment and absent language (NEDMIAL) [MIM:617804]: An autosomal dominant neurodevelopmental disorder characterized by global developmental delay, intellectual disability, severe speech impairment and gait abnormalities. {ECO:0000269|PubMed:28327206, ECO:0000269|PubMed:29100085}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Recessive Scores

• pRec: 0.134

Intolerance Scores

• loftool: 0.00648
• rvis_EVS: -1.51
• rvis_percentile_EVS: 3.54

Haploinsufficiency Scores

• pHI: 0.560
• hipred: Y
• hipred_score: 0.831
• ghis: 0.681

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: K
• gene_indispensability_pred: E
• gene_indispensability_score: 0.961

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Dhx30
• Phenotype: mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); embryo phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); growth/size/body region phenotype; homeostasis/metabolism phenotype

Gene ontology

• Biological process: central nervous system development;DNA duplex unwinding;mitochondrial large ribosomal subunit assembly
• Cellular component: nucleus;cytoplasm;mitochondrion;cytosol;ribonucleoprotein granule;mitochondrial nucleoid
• Molecular function: G-quadruplex RNA binding;chromatin binding;RNA binding;double-stranded RNA binding;ATP-dependent DNA helicase activity;ATP-dependent RNA helicase activity;protein binding;ATP binding;ATP-dependent 3'-5' RNA helicase activity