RPUSD2

RNA pseudouridine synthase domain containing 2, the group of Pseudouridine synthases|RNA pseudouridylate synthase domain containing

Basic information

Region (hg38): 15:40569299-40574949

Previous symbols: [ "C15orf19" ]

Links

ENSG00000166133 ∙ NCBI:27079 ∙ ∙ HGNC:24180 ∙ Uniprot:Q8IZ73 ∙ 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 RPUSD2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RPUSD2 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			50	2		52
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	50	2	0

Variants in RPUSD2

This is a list of pathogenic ClinVar variants found in the RPUSD2 region.

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

Position	Type	Phenotype	Significance	ClinVar
15-40569357-G-A		not specified	Uncertain significance (Aug 30, 2022)
15-40569360-G-T		not specified	Uncertain significance (Apr 07, 2023)
15-40569375-G-A		not specified	Uncertain significance (Nov 09, 2024)
15-40569499-G-C		not specified	Uncertain significance (Mar 25, 2024)
15-40569512-G-C		not specified	Uncertain significance (Nov 08, 2022)
15-40569522-A-C		not specified	Uncertain significance (Oct 25, 2023)
15-40569579-C-G		not specified	Uncertain significance (Dec 12, 2024)
15-40569602-C-T		not specified	Uncertain significance (Feb 15, 2023)
15-40569623-C-T		not specified	Uncertain significance (Dec 11, 2023)
15-40569624-C-T		not specified	Uncertain significance (Oct 03, 2022)
15-40569639-A-T		not specified	Uncertain significance (Nov 21, 2023)
15-40569641-C-T		not specified	Uncertain significance (Oct 04, 2022)
15-40569674-C-T		not specified	Uncertain significance (Oct 24, 2023)
15-40569695-G-A		not specified	Uncertain significance (Mar 07, 2024)
15-40569720-T-G		not specified	Uncertain significance (Oct 26, 2021)
15-40569762-T-G		not specified	Uncertain significance (Feb 22, 2025)
15-40569804-G-T		not specified	Uncertain significance (Jan 29, 2024)
15-40569887-G-A		not specified	Uncertain significance (May 02, 2024)
15-40571668-G-A		not specified	Uncertain significance (Jul 30, 2024)
15-40571713-C-T		not specified	Uncertain significance (Sep 13, 2023)
15-40571718-A-G		not specified	Uncertain significance (Aug 19, 2024)
15-40571727-C-G		not specified	Uncertain significance (Aug 21, 2024)
15-40571739-C-T		not specified	Uncertain significance (Apr 23, 2024)
15-40571766-A-G		not specified	Uncertain significance (Sep 14, 2022)
15-40571832-G-C		not specified	Uncertain significance (Apr 25, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RPUSD2	protein_coding	protein_coding	ENST00000315616	3	5161

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
8.80e-7	0.767	125715	0	32	125747	0.000127

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0734	313	317	0.988	0.0000178	3475
Missense in Polyphen		118	135.21	0.8727		1437
Synonymous	0.869	114	126	0.902	0.00000647	1156
Loss of Function	1.29	12	17.9	0.671	0.00000107	195

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000323	0.000323
Ashkenazi Jewish	0.000397	0.000397
East Asian	0.000109	0.000109
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000981	0.0000967
Middle Eastern	0.000109	0.000109
South Asian	0.0000980	0.0000980
Other	0.000326	0.000326

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0736

Intolerance Scores

• loftool: 0.726
• rvis_EVS: -0.62
• rvis_percentile_EVS: 17.31

Haploinsufficiency Scores

• pHI: 0.0338
• hipred: N
• hipred_score: 0.167
• ghis: 0.560

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0541

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rpusd2

Gene ontology

• Biological process: enzyme-directed rRNA pseudouridine synthesis;biological_process
• Cellular component: cellular_component
• Molecular function: RNA binding;pseudouridine synthase activity