RPUSD4

RNA pseudouridine synthase D4, the group of Pseudouridine synthases|RNA pseudouridylate synthase domain containing

Basic information

Region (hg38): 11:126202095-126211692

Links

ENSG00000165526 ∙ NCBI:84881 ∙ OMIM:617488 ∙ HGNC:25898 ∙ Uniprot:Q96CM3 ∙ 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 RPUSD4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RPUSD4 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						0
missense			19	6		25
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	19	6	0

Variants in RPUSD4

This is a list of pathogenic ClinVar variants found in the RPUSD4 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-126203482-C-T		not specified	Uncertain significance (Oct 29, 2021)
11-126203488-C-T		not specified	Uncertain significance (Dec 09, 2023)
11-126203512-C-T		not specified	Likely benign (Jun 05, 2024)
11-126203513-G-A		not specified	Uncertain significance (Jul 25, 2023)
11-126203538-T-G		not specified	Likely benign (Mar 12, 2024)
11-126203588-G-C		not specified	Uncertain significance (May 07, 2024)
11-126203647-A-C		not specified	Uncertain significance (May 15, 2023)
11-126203651-A-G		not specified	Likely benign (Aug 08, 2022)
11-126204272-C-T		not specified	Uncertain significance (Feb 28, 2023)
11-126204274-A-G		not specified	Uncertain significance (May 20, 2024)
11-126205470-G-A		not specified	Uncertain significance (Jun 11, 2021)
11-126205474-T-C		not specified	Likely benign (Jun 09, 2022)
11-126205495-C-T		not specified	Uncertain significance (May 30, 2024)
11-126205504-G-C		not specified	Uncertain significance (Apr 19, 2024)
11-126205557-C-T		not specified	Likely benign (Mar 07, 2023)
11-126205570-C-T		not specified	Uncertain significance (Mar 02, 2023)
11-126205582-C-T		not specified	Likely benign (Jun 07, 2022)
11-126205603-A-G		not specified	Uncertain significance (Nov 30, 2022)
11-126205741-C-T		not specified	Uncertain significance (Mar 29, 2022)
11-126205758-A-G		not specified	Uncertain significance (Nov 29, 2021)
11-126209627-G-A		not specified	Uncertain significance (Jan 08, 2024)
11-126209639-G-T		not specified	Uncertain significance (Apr 18, 2023)
11-126210916-T-C		not specified	Uncertain significance (Aug 02, 2021)
11-126210928-A-G		not specified	Uncertain significance (Sep 21, 2023)
11-126211017-T-C		not specified	Uncertain significance (Nov 22, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RPUSD4	protein_coding	protein_coding	ENST00000298317	7	9595

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.73e-7	0.638	125418	0	328	125746	0.00131

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.402	244	227	1.08	0.0000125	2423
Missense in Polyphen		68	67.889	1.0016		749
Synonymous	-0.395	97	92.2	1.05	0.00000494	782
Loss of Function	1.07	12	16.7	0.717	7.21e-7	185

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00113	0.00110
Ashkenazi Jewish	0.00395	0.00368
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.00231	0.00214
Middle Eastern	0.0000544	0.0000544
South Asian	0.000387	0.000359
Other	0.00176	0.00163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Catalyzes uridine to pseudouridine isomerization (pseudouridylation) of different mitochondrial RNA substrates. Acts on position 1397 in 16S mitochondrial ribosomal RNA (16S mt- rRNA). This modification is required for the assembly of 16S mt- rRNA into a functional mitochondrial ribosome (PubMed:27974379). Acts on position 39 in mitochondrial tRNA(Phe) (PubMed:28082677). As a component of a functional protein-RNA module, consisting of RCC1L, NGRN, RPUSD3, RPUSD4, TRUB2, FASTKD2 and 16S mt-rRNA, controls 16S mt-rRNA abundance and is required for intra- mitochondrial translation (PubMed:27667664). {ECO:0000269|PubMed:27667664, ECO:0000269|PubMed:27974379, ECO:0000269|PubMed:28082677}.

Recessive Scores

• pRec: 0.0821

Intolerance Scores

• loftool: 0.853
• rvis_EVS: 1
• rvis_percentile_EVS: 90.65

Haploinsufficiency Scores

• pHI: 0.0613
• hipred: N
• hipred_score: 0.169
• ghis: 0.399

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.662

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rpusd4

Gene ontology

• Biological process: pseudouridine synthesis;tRNA processing;positive regulation of mitochondrial translation
• Cellular component: mitochondrial matrix
• Molecular function: RNA binding;protein binding;pseudouridine synthase activity