PUSL1

pseudouridine synthase like 1, the group of Pseudouridine synthases

Basic information

Region (hg38): 1:1308597-1311677

Links

ENSG00000169972 ∙ NCBI:126789 ∙ ∙ HGNC:26914 ∙ Uniprot:Q8N0Z8 ∙ 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 PUSL1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PUSL1 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			45	5		50
nonsense			1			1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	46	5	0

Variants in PUSL1

This is a list of pathogenic ClinVar variants found in the PUSL1 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-1308654-C-T		not specified	Likely benign (Dec 11, 2024)
1-1308657-C-A		not specified	Likely benign (Oct 30, 2023)
1-1308659-G-T		not specified	Uncertain significance (Jul 02, 2024)
1-1308666-G-A		not specified	Uncertain significance (Feb 22, 2025)
1-1308926-C-T		not specified	Uncertain significance (Sep 07, 2022)
1-1308935-G-T		not specified	Uncertain significance (Jan 22, 2025)
1-1308937-A-G		not specified	Likely benign (Oct 08, 2024)
1-1308943-C-A		not specified	Uncertain significance (May 08, 2023)
1-1308943-C-T		not specified	Uncertain significance (Oct 25, 2022)
1-1308955-G-A		not specified	Uncertain significance (Mar 13, 2023)
1-1308965-A-T		not specified	Uncertain significance (Dec 03, 2024)
1-1309108-C-G		not specified	Uncertain significance (Aug 01, 2024)
1-1309119-G-A		not specified	Uncertain significance (Sep 26, 2022)
1-1309134-T-A		not specified	Uncertain significance (Mar 07, 2024)
1-1309139-C-A		not specified	Uncertain significance (Nov 03, 2022)
1-1309152-G-A		not specified	Uncertain significance (Mar 11, 2025)
1-1309161-G-C		not specified	Uncertain significance (Jun 16, 2023)
1-1309182-C-G		not specified	Uncertain significance (Aug 22, 2023)
1-1309210-C-T		not specified	Uncertain significance (Dec 06, 2024)
1-1309218-C-G		not specified	Uncertain significance (Jul 14, 2024)
1-1309221-C-T		not specified	Uncertain significance (Jan 17, 2024)
1-1309222-C-G		not specified	Uncertain significance (Apr 24, 2023)
1-1309238-G-C		not specified	Uncertain significance (Oct 04, 2024)
1-1309516-C-G		not specified	Uncertain significance (Apr 18, 2023)
1-1309527-C-T		not specified	Uncertain significance (Oct 01, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PUSL1	protein_coding	protein_coding	ENST00000379031	8	3111

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.65e-20	0.0000203	125150	0	163	125313	0.000651

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.44	217	165	1.32	0.00000989	1874
Missense in Polyphen		63	50.515	1.2472		589
Synonymous	-3.61	113	73.6	1.54	0.00000456	646
Loss of Function	-3.21	23	11.3	2.03	5.59e-7	141

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00371	0.00363
Ashkenazi Jewish	0.00	0.00
East Asian	0.000228	0.000218
Finnish	0.00191	0.00180
European (Non-Finnish)	0.000462	0.000451
Middle Eastern	0.000228	0.000218
South Asian	0.0000696	0.0000653
Other	0.000338	0.000327

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.142

Haploinsufficiency Scores

• pHI: 0.178
• hipred: N
• hipred_score: 0.197
• ghis: 0.489

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.930

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pusl1

Gene ontology

• Biological process: tRNA pseudouridine synthesis
• Cellular component: intracellular membrane-bounded organelle
• Molecular function: RNA binding;pseudouridine synthase activity