RPUSD3

RNA pseudouridine synthase D3, the group of RNA pseudouridylate synthase domain containing|Pseudouridine synthases

Basic information

Region (hg38): 3:9837849-9844602

Links

ENSG00000156990 ∙ NCBI:285367 ∙ OMIM:617759 ∙ HGNC:28437 ∙ Uniprot:Q6P087 ∙ 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 RPUSD3 gene.

• not_specified (49 variants)
• Inborn_genetic_diseases (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RPUSD3 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000173659.5. 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	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				1		1
missense		2	45	3		50
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	2	45	4	0

Highest pathogenic variant AF is 0.000009577089

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RPUSD3	protein_coding	protein_coding	ENST00000383820	9	6754

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.20e-7	0.712	125672	0	75	125747	0.000298

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.503	217	197	1.10	0.0000100	2184
Missense in Polyphen		33	45.168	0.7306		539
Synonymous	-0.748	92	83.3	1.10	0.00000386	794
Loss of Function	1.24	13	18.8	0.692	0.00000116	175

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000354	0.000354
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.000979	0.000979
Finnish	0.00	0.00
European (Non-Finnish)	0.000255	0.000255
Middle Eastern	0.000979	0.000979
South Asian	0.000523	0.000523
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Catalyzes uridine to pseudouridine isomerization (pseudouridylation) of specific mitochondrial mRNAs (mt-mRNAs), a post-transcriptional modification necessary for their translation. Acts at position 390 in COXI mt-mRNA and at position 697-699 in mitochondrial COXIII mt-mRNA (PubMed:27974379). As a component of a functional protein-RNA module, consisting of RCC1L, NGRN, RPUSD3, RPUSD4, TRUB2, FASTKD2 and 16S mitochondrial ribosomal RNA (16S mt-rRNA), controls 16S mt-rRNA abundance and may play a role in mitochondrial ribosome biogenesis (PubMed:27667664). {ECO:0000269|PubMed:27667664, ECO:0000269|PubMed:27974379}.

Recessive Scores

• pRec: 0.0740

Intolerance Scores

• loftool: 0.931
• rvis_EVS: 0.06
• rvis_percentile_EVS: 58.85

Haploinsufficiency Scores

• pHI: 0.104
• hipred: N
• hipred_score: 0.145
• ghis: 0.535

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: H
• gene_indispensability_pred: E
• gene_indispensability_score: 0.554

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rpusd3

Gene ontology

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