USP50

ubiquitin specific peptidase 50, the group of Ubiquitin specific peptidases

Basic information

Region (hg38): 15:50494017-50546708

Links

ENSG00000170236 ∙ NCBI:373509 ∙ ∙ HGNC:20079 ∙ Uniprot:Q70EL3 ∙ 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 USP50 gene.

• Inborn genetic diseases (14 variants)
• not provided (4 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the USP50 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					2	2
missense			14		1	15
nonsense						0
start loss						0
frameshift					1	1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	14	0	4

Variants in USP50

This is a list of pathogenic ClinVar variants found in the USP50 region.

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

Position	Type	Phenotype	Significance	ClinVar
15-50494133-G-A		Hereditary spastic paraplegia	Benign (Jan 25, 2024)
15-50494141-G-A		Hereditary spastic paraplegia	Uncertain significance (Nov 08, 2022)
15-50494145-G-A		Hereditary spastic paraplegia	Likely benign (Jul 06, 2022)
15-50494154-T-C		Hereditary spastic paraplegia	Likely benign (Dec 03, 2020)
15-50494246-T-C		Hereditary spastic paraplegia	Uncertain significance (Aug 27, 2021)
15-50494256-T-C			Likely benign (Apr 15, 2018)
15-50494282-T-TAAGA		Hereditary spastic paraplegia	Likely benign (Jan 18, 2024)
15-50495935-C-A		Hereditary spastic paraplegia	Uncertain significance (Mar 13, 2023)
15-50495943-T-C			Likely benign (Sep 10, 2018)
15-50496024-A-T			Likely benign (Dec 01, 2023)
15-50496031-G-C		Hereditary spastic paraplegia	Uncertain significance (Mar 18, 2022)
15-50496085-G-GTAAGT			Likely benign (Oct 16, 2017)
15-50497080-T-C		Hereditary spastic paraplegia	Likely benign (Oct 27, 2023)
15-50497164-C-T			Pathogenic (May 03, 2020)
15-50497165-G-A		Hereditary spastic paraplegia	Uncertain significance (Mar 10, 2021)
15-50497176-C-G		Hereditary spastic paraplegia	Uncertain significance (May 02, 2022)
15-50497211-G-A		Hereditary spastic paraplegia	Likely benign (Jul 01, 2022)
15-50497226-G-A		Hereditary spastic paraplegia	Benign (Jan 19, 2024)
15-50497247-T-G		Hereditary spastic paraplegia	Benign (Jan 12, 2024)
15-50497248-GTCC-G		Hereditary spastic paraplegia	Likely benign (Aug 10, 2023)
15-50498636-T-A		Hereditary spastic paraplegia	Uncertain significance (Nov 04, 2022)
15-50498662-T-G			Likely benign (Sep 17, 2017)
15-50498676-A-G		Hereditary spastic paraplegia	Uncertain significance (Jan 08, 2024)
15-50498687-C-G			not provided (-)
15-50498883-T-TTCTA		Hereditary spastic paraplegia	Benign (Jan 31, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
USP50	protein_coding	protein_coding	ENST00000532404	7	46147

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.63e-18	0.000305	123408	24	1210	124642	0.00496

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.390	165	180	0.918	0.00000922	2194
Missense in Polyphen		41	56.303	0.7282		753
Synonymous	0.190	67	69.0	0.971	0.00000397	605
Loss of Function	-1.52	23	16.4	1.40	6.87e-7	216

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0597	0.0599
Ashkenazi Jewish	0.00	0.00
East Asian	0.00123	0.00122
Finnish	0.000882	0.000882
European (Non-Finnish)	0.000711	0.000708
Middle Eastern	0.00123	0.00122
South Asian	0.00512	0.00498
Other	0.00199	0.00198

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Has no peptidase activity.

Recessive Scores

• pRec: 0.0994

Intolerance Scores

• loftool: 0.744
• rvis_EVS: 0.4
• rvis_percentile_EVS: 76.31

Haploinsufficiency Scores

• pHI: 0.0968
• hipred: N
• hipred_score: 0.170

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.364

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Usp50
• Phenotype: vision/eye phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span)

Gene ontology

• Biological process: ubiquitin-dependent protein catabolic process;endosome organization;Ras protein signal transduction;protein deubiquitination;positive regulation of protein homooligomerization;positive regulation of interleukin-18 production;positive regulation of interleukin-1 beta secretion;protein K63-linked deubiquitination;protein K48-linked deubiquitination;positive regulation of NLRP3 inflammasome complex assembly;positive regulation of cysteine-type endopeptidase activity
• Cellular component: cytosol;postsynaptic density;extrinsic component of plasma membrane;midbody;extrinsic component of endosome membrane;dendritic spine
• Molecular function: thiol-dependent ubiquitin-specific protease activity;ubiquitin-like protein-specific protease activity