PUSL1

protein-coding

pseudouridine synthase like 1, the group of Pseudouridine synthases

Gene summary

Predicted to enable pseudouridine synthase activity. Predicted to be involved in tRNA pseudouridine synthesis. Located in mitochondrion. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_153339.3

Inheritance

—

ClinVar variants

U:83B:6

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 2.03

Max pathogenic AF

—

Genomic locus

chr1:1,308,597-1,311,677

External References & Databases

Ensembl (ENSG00000169972)

Transcript & Mutation Effects

hg38 • Region Span ~3.1 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to PUSL1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 80

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_153339.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			76 clinvar	6 clinvar		82
nonsense			1 clinvar			1
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)			5 clinvar			5
Total	0	0	83	6	0	89

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 17 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_153339.3	RefSeq	NP_699170.1	8	MANE Select
ENST00000379031.10	Ensembl	ENSP00000368318.5	8	MANE Select
NM_001346116.2	RefSeq	NP_001333045.1	8	Standard
ENST00000467712.1	Ensembl	ENSP00000462968.1	3	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

tRNA pseudouridine synthesis

Molecular Function

RNA binding
pseudouridine synthase activity

Cellular Component

intracellular membrane-bounded organelle

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000379031
Coding exons: 8
Length: 3111
Individuals with no LoFs: 125150
Homozygous LoFs: 0
Heterozygous LoFs: 163
Defined: 125313
p: 0.000651

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-1.44	217	165	1.32	0.00000989	1874
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0034	0.0033	notable
Latino/Admixed American	0.00035	0.00035	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00023	0.00022	rare
Finnish	0.0019	0.0018	notable
European (Non-Finnish)	0.00046	0.00045	rare
South Asian	0.000070	0.000065	rare
Other	0.00034	0.00033	rare

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.142

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.930

Gene Damage Prediction

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