PUS7L

pseudouridine synthase 7 like, the group of Pseudouridine synthases

Basic information

Region (hg38): 12:43718991-43758793

Links

ENSG00000129317 ∙ NCBI:83448 ∙ ∙ HGNC:25276 ∙ Uniprot:Q9H0K6 ∙ 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 PUS7L gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PUS7L 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			47	1		48
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	47	1	0

Variants in PUS7L

This is a list of pathogenic ClinVar variants found in the PUS7L region.

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

Position	Type	Phenotype	Significance	ClinVar
12-43730435-G-A		not specified	Uncertain significance (Jan 18, 2022)
12-43730438-C-T		not specified	Uncertain significance (Feb 24, 2022)
12-43730543-G-A		not specified	Uncertain significance (Dec 27, 2022)
12-43730560-T-C		not specified	Uncertain significance (Oct 22, 2021)
12-43730591-G-A		not specified	Uncertain significance (Mar 21, 2022)
12-43730653-A-T		not specified	Uncertain significance (Jul 14, 2021)
12-43731707-G-C		not specified	Uncertain significance (Jan 19, 2022)
12-43736385-C-T		not specified	Uncertain significance (Apr 25, 2023)
12-43736457-T-C		not specified	Uncertain significance (Nov 10, 2022)
12-43736470-T-C		not specified	Uncertain significance (Mar 15, 2024)
12-43736522-T-C		not specified	Uncertain significance (Apr 27, 2024)
12-43736528-C-T		not specified	Uncertain significance (Oct 21, 2021)
12-43736530-T-C		not specified	Uncertain significance (Nov 30, 2022)
12-43736566-C-T		not specified	Uncertain significance (Feb 14, 2023)
12-43736587-G-A		not specified	Uncertain significance (Jul 11, 2023)
12-43736589-T-G		not specified	Uncertain significance (Oct 05, 2021)
12-43736653-T-C		not specified	Uncertain significance (Nov 19, 2022)
12-43742528-G-A		not specified	Uncertain significance (Aug 08, 2022)
12-43742536-T-A		not specified	Uncertain significance (Mar 13, 2023)
12-43742550-T-A		not specified	Uncertain significance (Sep 01, 2021)
12-43746212-T-A		not specified	Uncertain significance (Sep 21, 2023)
12-43748535-G-A		not specified	Uncertain significance (Aug 08, 2022)
12-43748555-G-C		not specified	Uncertain significance (Jul 19, 2023)
12-43748597-C-A		not specified	Uncertain significance (Dec 15, 2022)
12-43754387-G-A		not specified	Uncertain significance (Apr 12, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PUS7L	protein_coding	protein_coding	ENST00000416848	8	30211

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000259	0.982	125588	0	160	125748	0.000636

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.201	367	356	1.03	0.0000172	4685
Missense in Polyphen		88	98.014	0.89783		1276
Synonymous	0.896	113	126	0.898	0.00000639	1255
Loss of Function	2.16	13	24.5	0.530	0.00000111	372

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00303	0.00292
Ashkenazi Jewish	0.00	0.00
East Asian	0.00349	0.00327
Finnish	0.00	0.00
European (Non-Finnish)	0.000174	0.000167
Middle Eastern	0.00349	0.00327
South Asian	0.000996	0.000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Pseudouridylate synthase that catalyzes pseudouridylation of RNAs. {ECO:0000250|UniProtKB:Q96PZ0}.

Intolerance Scores

• loftool: 0.991
• rvis_EVS: 0.65
• rvis_percentile_EVS: 84.12

Haploinsufficiency Scores

• pHI: 0.214
• hipred: N
• hipred_score: 0.280
• ghis: 0.507

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0678

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pus7l

Gene ontology

• Biological process: pseudouridine synthesis
• Cellular component: nucleus
• Molecular function: RNA binding;protein binding;pseudouridine synthase activity