DDX31

DEAD-box helicase 31, the group of DEAD-box helicases|Protein phosphatase 1 regulatory subunits

Basic information

Region (hg38): 9:132592997-132670401

Links

ENSG00000125485 ∙ NCBI:64794 ∙ OMIM:616533 ∙ HGNC:16715 ∙ Uniprot:Q9H8H2 ∙ 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 DDX31 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DDX31 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			39	1		40
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			8			8
Total	0	0	47	2	0

Variants in DDX31

This is a list of pathogenic ClinVar variants found in the DDX31 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-132594873-T-C		not specified	Uncertain significance (Mar 06, 2023)
9-132594888-C-T		not specified	Uncertain significance (Mar 29, 2023)
9-132594940-G-T		not specified	Uncertain significance (May 28, 2024)
9-132594957-G-A		not specified	Uncertain significance (Dec 17, 2023)
9-132594997-C-T		not specified	Uncertain significance (Oct 09, 2024)
9-132595005-T-C		not specified	Uncertain significance (May 26, 2023)
9-132595022-G-C			Likely benign (Oct 01, 2022)
9-132595089-T-C		not specified	Uncertain significance (Sep 21, 2023)
9-132612100-C-T		not specified	Uncertain significance (Oct 22, 2021)
9-132612126-C-G		not specified	Uncertain significance (Feb 11, 2022)
9-132618342-A-G		not specified	Uncertain significance (Mar 19, 2024)
9-132618360-T-C		not specified	Uncertain significance (Sep 17, 2021)
9-132618386-G-A		not specified	Uncertain significance (Aug 17, 2021)
9-132618404-C-T		not specified	Uncertain significance (Mar 16, 2022)
9-132618432-C-A		not specified	Uncertain significance (May 16, 2024)
9-132625665-T-C		not specified	Uncertain significance (Nov 09, 2024)
9-132625698-T-C		not specified	Uncertain significance (Jun 16, 2023)
9-132625744-C-T		not specified	Uncertain significance (Jul 27, 2024)
9-132630303-T-C		not specified	Uncertain significance (Aug 30, 2024)
9-132630349-G-A		not specified	Uncertain significance (Apr 04, 2024)
9-132630366-C-T		not specified	Uncertain significance (May 05, 2023)
9-132630367-G-A		not specified	Uncertain significance (Dec 19, 2022)
9-132632079-G-A		not specified	Uncertain significance (Jul 27, 2024)
9-132642060-T-C		not specified	Uncertain significance (Oct 04, 2022)
9-132645923-A-G		not specified	Uncertain significance (Jan 09, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DDX31	protein_coding	protein_coding	ENST00000372159	20	77405

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.98e-12	0.989	125657	0	91	125748	0.000362

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0334	478	480	0.996	0.0000273	5459
Missense in Polyphen		131	151.09	0.86701		1727
Synonymous	-0.906	212	196	1.08	0.0000118	1713
Loss of Function	2.53	26	44.2	0.589	0.00000242	492

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00103	0.00103
Ashkenazi Jewish	0.00	0.00
East Asian	0.00125	0.00125
Finnish	0.000139	0.000139
European (Non-Finnish)	0.000282	0.000281
Middle Eastern	0.00125	0.00125
South Asian	0.000230	0.000229
Other	0.000333	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Probable ATP-dependent RNA helicase (By similarity). Plays a role in ribosome biogenesis and TP53/p53 regulation through its interaction with NPM1 (PubMed:23019224). {ECO:0000250, ECO:0000269|PubMed:23019224}.

Recessive Scores

• pRec: 0.0767

Intolerance Scores

• loftool: 0.896
• rvis_EVS: 1
• rvis_percentile_EVS: 90.79

Haploinsufficiency Scores

• pHI: 0.247
• hipred: Y
• hipred_score: 0.541
• ghis: 0.462

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0910

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ddx31

Gene ontology

• Biological process: ribosome biogenesis
• Cellular component: nucleolus;Golgi apparatus;intracellular membrane-bounded organelle
• Molecular function: RNA binding;helicase activity;protein binding;ATP binding