RPUSD1

RNA pseudouridine synthase domain containing 1, the group of Pseudouridine synthases|RNA pseudouridylate synthase domain containing

Basic information

Region (hg38): 16:784973-788397

Previous symbols: [ "C16orf40" ]

Links

ENSG00000007376 ∙ NCBI:113000 ∙ ∙ HGNC:14173 ∙ Uniprot:Q9UJJ7 ∙ 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 RPUSD1 gene.

• Inborn genetic diseases (24 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RPUSD1 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			23	1		24
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	23	2	0

Variants in RPUSD1

This is a list of pathogenic ClinVar variants found in the RPUSD1 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-785960-G-A		not specified	Uncertain significance (Nov 08, 2021)
16-785973-A-G		not specified	Uncertain significance (Jul 26, 2022)
16-786029-G-A		not specified	Uncertain significance (Dec 31, 2023)
16-786030-T-C		not specified	Uncertain significance (Mar 27, 2023)
16-786047-C-T		not specified	Uncertain significance (Jan 31, 2022)
16-786051-C-A		not specified	Uncertain significance (Nov 30, 2022)
16-786116-G-A		not specified	Uncertain significance (Apr 14, 2023)
16-786119-G-T		not specified	Uncertain significance (Apr 22, 2022)
16-786120-T-A		not specified	Uncertain significance (Jun 27, 2023)
16-786139-G-C			Likely benign (Apr 01, 2023)
16-786152-G-A		not specified	Uncertain significance (Oct 24, 2023)
16-786153-A-G		not specified	Likely benign (Dec 19, 2022)
16-786195-G-A		not specified	Uncertain significance (Nov 09, 2023)
16-786204-G-A		not specified	Uncertain significance (Oct 04, 2022)
16-786212-G-A		not specified	Uncertain significance (May 04, 2023)
16-786231-C-T		not specified	Uncertain significance (Dec 27, 2023)
16-786263-T-C		not specified	Uncertain significance (May 15, 2023)
16-786272-A-G		not specified	Uncertain significance (Dec 14, 2023)
16-786293-C-T		not specified	Likely benign (Feb 14, 2023)
16-786309-C-T		not specified	Uncertain significance (Sep 28, 2021)
16-786341-A-G		not specified	Uncertain significance (Jun 09, 2022)
16-786359-C-T		not specified	Uncertain significance (Jun 24, 2022)
16-786368-T-C		Malignant tumor of prostate	Uncertain significance (-)
16-786850-T-C		not specified	Uncertain significance (Sep 14, 2023)
16-786905-G-C		not specified	Uncertain significance (Jan 10, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RPUSD1	protein_coding	protein_coding	ENST00000561734	5	3424

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.67e-10	0.0171	125381	0	67	125448	0.000267

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.49	277	216	1.29	0.0000154	1978
Missense in Polyphen		114	85.596	1.3318		819
Synonymous	-5.48	170	100	1.70	0.00000767	671
Loss of Function	-1.03	13	9.56	1.36	4.07e-7	107

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000303	0.000302
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.000488	0.000477
Middle Eastern	0.0000544	0.0000544
South Asian	0.000165	0.000163
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.132

Intolerance Scores

• loftool: 0.672
• rvis_EVS: -0.24
• rvis_percentile_EVS: 36.17

Haploinsufficiency Scores

• pHI: 0.0964
• hipred: N
• hipred_score: 0.251
• ghis: 0.554

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.382

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rpusd1

Gene ontology

• Biological process: pseudouridine synthesis;biological_process
• Cellular component: cellular_component
• Molecular function: molecular_function;RNA binding;pseudouridine synthase activity