USP49

ubiquitin specific peptidase 49, the group of Ubiquitin specific peptidases

Basic information

Region (hg38): 6:41789896-41895375

Links

ENSG00000164663 ∙ NCBI:25862 ∙ ∙ HGNC:20078 ∙ Uniprot:Q70CQ1 ∙ 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 USP49 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the USP49 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			33	1	1	35
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	33	1	1

Variants in USP49

This is a list of pathogenic ClinVar variants found in the USP49 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-41798841-T-C		not specified	Uncertain significance (Mar 07, 2023)
6-41798842-G-T		not specified	Uncertain significance (Mar 23, 2023)
6-41798886-C-T		not specified	Uncertain significance (Sep 24, 2024)
6-41799889-T-G		not specified	Uncertain significance (Feb 21, 2024)
6-41799920-T-C		not specified	Uncertain significance (Jun 28, 2024)
6-41799924-A-G		not specified	Uncertain significance (May 31, 2022)
6-41803824-C-T		not specified	Uncertain significance (Jun 16, 2023)
6-41803837-T-G		not specified	Uncertain significance (Oct 25, 2022)
6-41803973-A-G		not specified	Uncertain significance (Jun 26, 2024)
6-41805698-G-C		not specified	Uncertain significance (Nov 18, 2022)
6-41805800-T-C		not specified	Uncertain significance (Aug 08, 2023)
6-41805863-G-A		not specified	Uncertain significance (May 04, 2022)
6-41805972-T-C		not specified	Uncertain significance (Nov 17, 2022)
6-41805990-A-G		not specified	Uncertain significance (May 10, 2022)
6-41805998-C-A		not specified	Uncertain significance (Oct 06, 2021)
6-41806027-A-C		not specified	Uncertain significance (Oct 05, 2022)
6-41806049-G-A		not specified	Uncertain significance (Sep 16, 2021)
6-41806056-T-C		not specified	Uncertain significance (May 12, 2024)
6-41806253-C-A		not specified	Uncertain significance (Feb 06, 2024)
6-41806268-G-C		not specified	Uncertain significance (Oct 13, 2023)
6-41806269-T-G		not specified	Uncertain significance (Jan 03, 2024)
6-41806281-C-G		not specified	Uncertain significance (Mar 29, 2023)
6-41806301-G-T		not specified	Uncertain significance (Nov 25, 2024)
6-41806322-G-A		not specified	Uncertain significance (Feb 14, 2023)
6-41806401-G-C		not specified	Uncertain significance (May 09, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
USP49	protein_coding	protein_coding	ENST00000373006	4	105466

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.938	0.0617	125740	0	8	125748	0.0000318

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.62	271	423	0.641	0.0000291	4100
Missense in Polyphen		86	193.06	0.44546		2005
Synonymous	0.371	181	187	0.966	0.0000134	1349
Loss of Function	4.05	4	26.5	0.151	0.00000157	271

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000291	0.0000291
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000539	0.0000439
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Specifically deubiquitinates histone H2B at 'Lys-120' (H2BK120Ub). H2BK120Ub is a specific tag for epigenetic transcriptional activation and acts as a regulator of mRNA splicing. Deubiquitination is required for efficient cotranscriptional splicing of a large set of exons. {ECO:0000269|PubMed:23824326}.
• Pathway: Post-translational protein modification;Metabolism of proteins;Ub-specific processing proteases;Deubiquitination (Consensus)

Recessive Scores

• pRec: 0.121

Intolerance Scores

• loftool: 0.278
• rvis_EVS: 0
• rvis_percentile_EVS: 53.73

Haploinsufficiency Scores

• pHI: 0.490
• hipred: Y
• hipred_score: 0.728
• ghis: 0.595

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.598

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Usp49

Gene ontology

• Biological process: mRNA splicing, via spliceosome;ubiquitin-dependent protein catabolic process;protein deubiquitination;histone H2B conserved C-terminal lysine deubiquitination
• Cellular component: nucleoplasm;cytoplasm
• Molecular function: cysteine-type endopeptidase activity;thiol-dependent ubiquitin-specific protease activity;protein binding;zinc ion binding;thiol-dependent ubiquitinyl hydrolase activity;histone binding