DHX38

DEAH-box helicase 38, the group of DEAH-box helicases

Basic information

Region (hg38): 16:72093613-72112912

Previous symbols: [ "DDX38" ]

Links

ENSG00000140829 ∙ NCBI:9785 ∙ OMIM:605584 ∙ HGNC:17211 ∙ Uniprot:Q92620 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• retinitis pigmentosa 84 (Strong), mode of inheritance: AR
• retinitis pigmentosa (Supportive), mode of inheritance: AD
• retinitis pigmentosa 84 (Limited), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Retinitis pigmentosa 84	AR	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	Ophthalmologic	24737827; 30208423

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the DHX38 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DHX38 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			9	219	13	241
missense		2	347	9	3	361
nonsense		1	12			13
start loss						0
frameshift			6			6
inframe indel			4			4
splice donor/acceptor (+/-2bp)			4			4
splice region			22	35	3	60
non coding			1	91	9	101
Total	0	3	383	319	25

Variants in DHX38

This is a list of pathogenic ClinVar variants found in the DHX38 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-72096163-G-A			Likely benign (Jul 28, 2023)
16-72096167-A-T			Uncertain significance (Mar 23, 2021)
16-72096184-G-A			Likely benign (Sep 15, 2021)
16-72096189-A-G			Uncertain significance (May 27, 2022)
16-72096191-C-G			Uncertain significance (May 20, 2022)
16-72096191-C-T			Uncertain significance (Feb 09, 2022)
16-72096196-G-A			Likely benign (May 05, 2023)
16-72096204-C-G			Benign (Jan 31, 2024)
16-72096212-G-A		Retinitis pigmentosa 84 • Retinal dystrophy	Uncertain significance (Jan 01, 2023)
16-72096219-AGGTTGGT-A			Uncertain significance (Jun 24, 2022)
16-72096221-G-A			Uncertain significance (Aug 28, 2021)
16-72096225-G-C		not specified	Uncertain significance (Dec 11, 2023)
16-72096226-T-C		Retinal dystrophy	Benign (Jan 31, 2024)
16-72096241-G-A		not specified • DHX38-related disorder	Benign (Jan 19, 2024)
16-72096246-A-G			Uncertain significance (Jul 30, 2022)
16-72096250-T-C			Likely benign (Dec 04, 2023)
16-72096252-C-T			Uncertain significance (Apr 24, 2023)
16-72096253-G-A			Likely benign (Sep 27, 2022)
16-72096255-C-T			Uncertain significance (Feb 24, 2022)
16-72096259-C-T			Likely benign (Jul 19, 2022)
16-72096280-T-C			Likely benign (Jun 13, 2023)
16-72096286-T-C			Likely benign (Jul 21, 2023)
16-72096290-C-T			Uncertain significance (Jul 15, 2022)
16-72096291-G-A		not specified	Uncertain significance (Feb 05, 2024)
16-72096292-C-A			Likely benign (Jun 13, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DHX38	protein_coding	protein_coding	ENST00000268482	26	19351

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.11e-12	1.00	125696	0	52	125748	0.000207

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.67	578	789	0.732	0.0000517	8012
Missense in Polyphen		166	297.44	0.5581		2957
Synonymous	0.192	312	316	0.986	0.0000213	2370
Loss of Function	4.27	32	70.8	0.452	0.00000404	755

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000300	0.000300
Ashkenazi Jewish	0.000199	0.000198
East Asian	0.000327	0.000326
Finnish	0.0000929	0.0000924
European (Non-Finnish)	0.000233	0.000229
Middle Eastern	0.000327	0.000326
South Asian	0.000262	0.000261
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Probable ATP-binding RNA helicase involved in pre-mRNA splicing.
• Pathway: Spliceosome - Homo sapiens (human);mRNA Processing;Gene expression (Transcription);RNA Polymerase II Transcription;Metabolism of RNA;Cleavage of Growing Transcript in the Termination Region ;RNA Polymerase II Transcription Termination;mRNA Splicing - Major Pathway;Transport of Mature mRNA derived from an Intron-Containing Transcript;mRNA Splicing;mRNA 3,-end processing;Transport of Mature Transcript to Cytoplasm;Processing of Capped Intron-Containing Pre-mRNA (Consensus)

Recessive Scores

• pRec: 0.140

Intolerance Scores

• loftool: 0.658
• rvis_EVS: -1.14
• rvis_percentile_EVS: 6.36

Haploinsufficiency Scores

• pHI: 0.102
• hipred: Y
• hipred_score: 0.648
• ghis: 0.571

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.835

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Dhx38

Gene ontology

• Biological process: mRNA splicing, via spliceosome;RNA export from nucleus;mRNA export from nucleus;mRNA 3'-end processing
• Cellular component: nucleus;nucleoplasm;membrane;catalytic step 2 spliceosome
• Molecular function: RNA binding;protein binding;ATP binding;ATP-dependent 3'-5' RNA helicase activity