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.

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.

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		2	18	2		22
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	2	18	2	0

Variants in RPUSD3

This is a list of pathogenic ClinVar variants found in the RPUSD3 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-9838027-G-A		not specified	Likely benign (Apr 14, 2022)
3-9838128-T-C		not specified	Uncertain significance (May 15, 2024)
3-9838156-C-T		not specified	Uncertain significance (Feb 07, 2023)
3-9838183-G-A		not specified	Uncertain significance (Apr 24, 2023)
3-9838185-C-T		not specified	Uncertain significance (Aug 13, 2021)
3-9839058-C-A		not specified	Uncertain significance (Feb 10, 2022)
3-9839076-G-T		not specified	Uncertain significance (Feb 28, 2024)
3-9839088-T-C		not specified	Uncertain significance (Jul 06, 2021)
3-9839148-G-A		Inborn genetic diseases	Likely pathogenic (-)
3-9840223-C-T		not specified	Uncertain significance (Jun 16, 2024)
3-9840238-G-A		Inborn genetic diseases	Likely pathogenic (-)
3-9840258-T-C		not specified	Uncertain significance (Jul 28, 2021)
3-9840755-C-T		not specified	Uncertain significance (Jun 05, 2023)
3-9841995-C-A		not specified	Uncertain significance (Oct 26, 2021)
3-9842046-G-A		not specified	Uncertain significance (Jan 10, 2022)
3-9842053-C-G		not specified	Uncertain significance (May 07, 2024)
3-9842064-G-A		not specified	Uncertain significance (Dec 21, 2023)
3-9842231-G-A		not specified	Uncertain significance (Jan 25, 2023)
3-9843468-T-C		not specified	Uncertain significance (Dec 08, 2023)
3-9843929-C-T		not specified	Uncertain significance (Mar 15, 2024)
3-9843932-A-T		not specified	Uncertain significance (May 17, 2023)
3-9843945-G-C		not specified	Uncertain significance (May 05, 2022)
3-9843951-A-G		not specified	Uncertain significance (May 24, 2023)
3-9843957-T-C		not specified	Likely benign (Feb 06, 2023)
3-9843968-C-A		not specified	Uncertain significance (Jun 28, 2023)

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