PUS10

pseudouridine synthase 10, the group of Pseudouridine synthases

Basic information

Region (hg38): 2:60940221-61018259

Previous symbols: [ "CCDC139" ]

Links

ENSG00000162927 ∙ NCBI:150962 ∙ OMIM:612787 ∙ HGNC:26505 ∙ Uniprot:Q3MIT2 ∙ 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 PUS10 gene.

• Peroxisome biogenesis disorder 11A (Zellweger) (54 variants)
• Inborn genetic diseases (24 variants)
• not provided (12 variants)
• not specified (2 variants)
• Peroxisome biogenesis disorder 11A (Zellweger);Peroxisome biogenesis disorder 11B (1 variants)
• Peroxisome biogenesis disorder 1A (Zellweger) (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PUS10 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			18	1		19
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding	2	1	30	18	2	53
Total	2	1	48	19	2

Highest pathogenic variant AF is 0.0000131

Variants in PUS10

This is a list of pathogenic ClinVar variants found in the PUS10 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-60942424-C-A		not specified	Uncertain significance (Sep 16, 2021)
2-60945046-A-G		not specified	Uncertain significance (Aug 20, 2023)
2-60948052-T-C		not specified	Uncertain significance (Jan 23, 2024)
2-60948093-C-G		not specified	Likely benign (Feb 28, 2023)
2-60948124-C-T		not specified	Uncertain significance (Nov 18, 2022)
2-60953955-G-A		not specified	Uncertain significance (Aug 04, 2021)
2-60954117-G-A		not specified	Uncertain significance (Mar 02, 2023)
2-60954144-T-C		not specified	Uncertain significance (Dec 17, 2023)
2-60954158-C-T		not specified	Uncertain significance (Jul 05, 2022)
2-60960445-G-A		not specified	Uncertain significance (Jan 17, 2024)
2-60960517-C-T		not specified	Uncertain significance (Jan 17, 2024)
2-60961505-C-T		not specified	Uncertain significance (Jan 05, 2022)
2-60961511-A-G		not specified	Uncertain significance (Nov 22, 2021)
2-60961528-T-C		not specified	Uncertain significance (Nov 09, 2021)
2-60961535-G-A		not specified	Uncertain significance (Aug 16, 2021)
2-60967512-A-G		not specified	Uncertain significance (Jun 14, 2022)
2-60971551-C-T		not specified	Uncertain significance (Nov 09, 2023)
2-61006576-G-T		not specified	Uncertain significance (Apr 18, 2023)
2-61006579-G-A		not specified	Uncertain significance (Dec 02, 2022)
2-61008836-C-A		not specified	Uncertain significance (Sep 16, 2021)
2-61008846-G-C		not specified	Uncertain significance (Sep 01, 2021)
2-61008858-T-C		not specified	Uncertain significance (Jan 04, 2024)
2-61008942-G-A		not specified	Uncertain significance (Jun 22, 2021)
2-61011809-A-T		not specified	Uncertain significance (Sep 07, 2022)
2-61011829-C-T		not specified	Uncertain significance (Oct 12, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PUS10	protein_coding	protein_coding	ENST00000316752	17	78038

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
7.88e-14	0.400	115833	0	9915	125748	0.0402

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0423	264	266	0.993	0.0000129	3489
Missense in Polyphen		73	84.142	0.86758		1055
Synonymous	-0.735	105	95.9	1.10	0.00000484	959
Loss of Function	1.37	25	33.6	0.745	0.00000175	408

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0626	0.0576
Ashkenazi Jewish	0.0146	0.0143
East Asian	0.0544	0.0496
Finnish	0.0535	0.0490
European (Non-Finnish)	0.0583	0.0546
Middle Eastern	0.0544	0.0496
South Asian	0.0115	0.0112
Other	0.0286	0.0272

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Pseudouridylate synthases catalyze pseudouridination of structural RNAs, including transfer, ribosomal, and splicing RNAs. PUS10 catalyzes the formation of the universal psi55 in the GC loop of transfer RNAs (Probable). Modulator of TRAIL-induced cell death via activation of procaspase 8 and BID cleavage. Required for the progression of the apoptotic signal through intrinsic mitochondrial cell death. {ECO:0000269|PubMed:14527409, ECO:0000269|PubMed:19712588, ECO:0000305}.

Recessive Scores

• pRec: 0.100

Intolerance Scores

• loftool: 0.451
• rvis_EVS: -0.49
• rvis_percentile_EVS: 22.51

Haploinsufficiency Scores

• pHI: 0.263
• hipred: N
• hipred_score: 0.292
• ghis: 0.592

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.402

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pus10

Gene ontology

• Biological process: tRNA pseudouridine synthesis
• Molecular function: RNA binding;pseudouridine synthase activity;tRNA pseudouridine synthase activity