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
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.

not_provided (138 variants)
Inborn_genetic_diseases (85 variants)
Neurodevelopmental_disorder_with_severe_motor_impairment_and_absent_language (55 variants)
DHX30-related_disorder (17 variants)
not_specified (9 variants)
Microcephaly (3 variants)
Intellectual_disability (3 variants)
Strabismus (2 variants)
Global_developmental_delay (2 variants)
See_cases (2 variants)
Short_stature (2 variants)
EEG_abnormality (1 variants)
Delayed_speech_and_language_development (1 variants)
Hereditary_ataxia (1 variants)
Sleep_abnormality (1 variants)
Axial_hypotonia (1 variants)
Oculomotor_apraxia (1 variants)
Seizure (1 variants)
Generalized_hypotonia (1 variants)
Hirsutism (1 variants)
Abnormal_cerebral_white_matter_morphology (1 variants)
Autism,_susceptiblity_to (1 variants)
Hearing_impairment (1 variants)
Autism (1 variants)
Unsteady_gait (1 variants)
Failure_to_thrive (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. These statistics are base on transcript: NM_000138615.3. 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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous			1 clinvar	35 clinvar	2 clinvar	38
missense	7 clinvar	7 clinvar	158 clinvar	33 clinvar	1 clinvar	206
nonsense	1 clinvar	3 clinvar	2 clinvar			6
start loss						0
frameshift	1 clinvar		7 clinvar			8
splice donor/acceptor (+/-2bp)	1 clinvar	1 clinvar	2 clinvar			4
Total	10	11	170	68	3

Highest pathogenic variant AF is 0.0000034294776

Loading clinvar variants...

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