DHX16

DEAH-box helicase 16, the group of Spliceosomal Bact complex|Spliceosomal P complex|DEAH-box helicases|Spliceosomal C complex

Basic information

Region (hg38): 6:30653119-30673006

Previous symbols: [ "DDX16" ]

Links

ENSG00000204560 ∙ NCBI:8449 ∙ OMIM:603405 ∙ HGNC:2739 ∙ Uniprot:O60231 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• neuromuscular disease and ocular or auditory anomalies with or without seizures (Strong), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Neuromuscular disease and ocular or auditory anomalies with or without seizures	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	Audiologic/Otolaryngologic; Musculoskeletal; Neurologic; Ophthalmologic	31256877

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the DHX16 gene.

• not provided (1 variants)
• Neurodevelopmental delay;Seizure;Intellectual disability (1 variants)
• Neuromuscular disease and ocular or auditory anomalies with or without seizures (1 variants)
• Neurodevelopmental disorders (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DHX16 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	6
missense	1	2	50	2	6	61
nonsense			1			1
start loss						0
frameshift			2			2
inframe indel			1			1
splice donor/acceptor (+/-2bp)			1			1
splice region			1	3		4
non coding					1	1
Total	1	2	55	5	10

Variants in DHX16

This is a list of pathogenic ClinVar variants found in the DHX16 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-30653370-C-T		Inborn genetic diseases	Uncertain significance (Dec 13, 2021)
6-30654719-T-C		Inborn genetic diseases	Uncertain significance (Jun 10, 2022)
6-30654817-C-G		DHX16-related disorder	Benign (Apr 01, 2022)
6-30654836-C-T		Inborn genetic diseases • Neuromuscular disease and ocular or auditory anomalies with or without seizures	Uncertain significance (Sep 17, 2021)
6-30654876-T-C		Neuromuscular disease and ocular or auditory anomalies with or without seizures	Uncertain significance (Mar 26, 2024)
6-30655180-G-A		Inborn genetic diseases • Neuromuscular disease and ocular or auditory anomalies with or without seizures	Uncertain significance (Sep 06, 2022)
6-30655209-C-T		Neuromuscular disease and ocular or auditory anomalies with or without seizures	Uncertain significance (Jan 28, 2021)
6-30655255-G-A		Inborn genetic diseases	Uncertain significance (Jan 24, 2023)
6-30655292-A-G		DHX16-related disorder	Benign (Sep 13, 2021)
6-30655493-C-T		Inborn genetic diseases	Uncertain significance (Jan 09, 2024)
6-30655494-G-A		Inborn genetic diseases	Uncertain significance (Dec 13, 2023)
6-30655530-G-A		Neuromuscular disease and ocular or auditory anomalies with or without seizures	Uncertain significance (Jul 30, 2021)
6-30655578-T-A		Inborn genetic diseases	Uncertain significance (Jul 19, 2022)
6-30656392-G-A		Inborn genetic diseases	Uncertain significance (Feb 06, 2023)
6-30656464-T-C		DHX16-related disorder	Benign (Oct 31, 2019)
6-30656474-G-C		Inborn genetic diseases	Likely benign (Mar 19, 2024)
6-30656605-T-C			Uncertain significance (Nov 08, 2023)
6-30656656-G-A		Inborn genetic diseases	Uncertain significance (Apr 18, 2023)
6-30656699-G-T		Inborn genetic diseases	Uncertain significance (Jan 08, 2024)
6-30656763-G-T		DHX16-related disorder	Likely benign (Nov 21, 2019)
6-30656974-A-G		Inborn genetic diseases	Uncertain significance (Oct 20, 2022)
6-30656992-C-T		Inborn genetic diseases	Uncertain significance (Dec 12, 2023)
6-30657004-C-T		Inborn genetic diseases	Uncertain significance (Feb 17, 2023)
6-30657009-C-A		Enlarged kidney;Multiple renal cysts;Reduced renal corticomedullary differentiation • Neuromuscular disease and ocular or auditory anomalies with or without seizures • Neurodevelopmental disorders	Pathogenic/Likely pathogenic (Jul 14, 2020)
6-30657035-C-T		Inborn genetic diseases	Uncertain significance (Dec 15, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DHX16	protein_coding	protein_coding	ENST00000376442	20	19919

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.60e-12	1.00	125604	0	144	125748	0.000573

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.08	417	635	0.656	0.0000417	6672
Missense in Polyphen		26	36.211	0.718		372
Synonymous	1.47	213	242	0.879	0.0000132	2141
Loss of Function	3.96	31	65.6	0.472	0.00000456	617

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00135	0.00129
Ashkenazi Jewish	0.00211	0.00199
East Asian	0.000773	0.000761
Finnish	0.000187	0.000185
European (Non-Finnish)	0.000514	0.000492
Middle Eastern	0.000773	0.000761
South Asian	0.000560	0.000555
Other	0.000522	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in pre-mRNA splicing. Contributes to pre-mRNA splicing after spliceosome formation and prior to the first transesterification reaction. {ECO:0000269|PubMed:20423332, ECO:0000269|PubMed:20841358, ECO:0000269|PubMed:25296192}.
• Pathway: Spliceosome - Homo sapiens (human);mRNA Processing;Metabolism of RNA;mRNA Splicing - Major Pathway;mRNA Splicing;Processing of Capped Intron-Containing Pre-mRNA (Consensus)

Recessive Scores

• pRec: 0.111

Intolerance Scores

• loftool: 0.946
• rvis_EVS: -0.02
• rvis_percentile_EVS: 52.25

Haploinsufficiency Scores

• pHI: 0.430
• hipred: Y
• hipred_score: 0.627
• ghis: 0.537

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: H
• gene_indispensability_pred: E
• gene_indispensability_score: 0.615

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Dhx16

Zebrafish Information Network

• Gene name: dhx16
• Affected structure: blastoderm
• Phenotype tag: abnormal
• Phenotype quality: increased thickness

Gene ontology

• Biological process: mRNA splicing, via spliceosome;RNA splicing
• Cellular component: nucleus;nucleoplasm;spliceosomal complex
• Molecular function: RNA binding;RNA helicase activity;protein binding;ATP binding;ATPase activity;ATP-dependent 3'-5' RNA helicase activity