USP44

ubiquitin specific peptidase 44, the group of Ubiquitin specific peptidases

Basic information

Region (hg38): 12:95516560-95551476

Links

ENSG00000136014 ∙ NCBI:84101 ∙ OMIM:610993 ∙ HGNC:20064 ∙ Uniprot:Q9H0E7 ∙ 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 USP44 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the USP44 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				1	2	3
missense			44	2	2	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	44	3	4

Variants in USP44

This is a list of pathogenic ClinVar variants found in the USP44 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-95518183-C-A		not specified	Uncertain significance (Dec 10, 2024)
12-95518212-A-C		not specified	Uncertain significance (Oct 28, 2024)
12-95518237-T-G		not specified	Uncertain significance (Aug 08, 2022)
12-95518281-T-A		not specified	Uncertain significance (Feb 28, 2023)
12-95521138-T-A		not specified	Uncertain significance (Jul 09, 2021)
12-95524736-T-G		not specified	Uncertain significance (Mar 03, 2025)
12-95524755-A-G		not specified	Uncertain significance (Nov 13, 2024)
12-95528831-T-C		not specified	Uncertain significance (Dec 11, 2023)
12-95528833-T-C		not specified	Uncertain significance (Jan 04, 2024)
12-95528837-C-T		not specified	Uncertain significance (Aug 02, 2021)
12-95528926-C-T		not specified	Uncertain significance (Jun 26, 2024)
12-95528942-A-G		USP44-related disorder	Likely benign (Apr 16, 2019)
12-95528962-T-C		not specified	Uncertain significance (Aug 12, 2024)
12-95528988-T-A		USP44-related disorder	Likely benign (Jul 19, 2019)
12-95532888-G-A		not specified	Uncertain significance (Jun 10, 2022)
12-95532998-G-T		not specified	Uncertain significance (Mar 07, 2025)
12-95533004-C-T		not specified	Uncertain significance (Nov 25, 2024)
12-95533041-G-C		not specified	Uncertain significance (Jun 25, 2024)
12-95533093-C-A		not specified	Uncertain significance (Dec 03, 2024)
12-95533116-G-C		not specified	Uncertain significance (Mar 31, 2024)
12-95533127-T-C		not specified	Uncertain significance (Sep 07, 2022)
12-95533159-C-A		not specified	Uncertain significance (May 31, 2023)
12-95533170-C-T		USP44-related disorder	Benign (Dec 26, 2018)
12-95533181-C-T		not specified	Uncertain significance (May 27, 2022)
12-95533182-C-T		not specified	Uncertain significance (Mar 01, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
USP44	protein_coding	protein_coding	ENST00000258499	5	34931

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
9.81e-15	0.248	125608	1	139	125748	0.000557

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.654	348	384	0.906	0.0000200	4671
Missense in Polyphen		101	116.33	0.86823		1459
Synonymous	0.745	126	137	0.919	0.00000725	1348
Loss of Function	1.23	26	33.7	0.772	0.00000204	382

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00243	0.00242
Ashkenazi Jewish	0.000198	0.000198
East Asian	0.000489	0.000489
Finnish	0.0000504	0.0000462
European (Non-Finnish)	0.000582	0.000563
Middle Eastern	0.000489	0.000489
South Asian	0.000264	0.000261
Other	0.000652	0.000652

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Deubiquitinase that plays a key regulatory role in the spindle assembly checkpoint or mitotic checkpoint by preventing premature anaphase onset. Acts by specifically mediating deubiquitination of CDC20, a negative regulator of the anaphase promoting complex/cyclosome (APC/C). Deubiquitination of CDC20 leads to stabilize the MAD2L1-CDC20-APC/C ternary complex (also named mitotic checkpoint complex), thereby preventing premature activation of the APC/C. Promotes association of MAD2L1 with CDC20 and reinforces the spindle assembly checkpoint. Acts as a negative regulator of histone H2B (H2BK120ub1) ubiquitination. {ECO:0000269|PubMed:17443180, ECO:0000269|PubMed:22681888}.
• Pathway: Post-translational protein modification;Metabolism of proteins;Ub-specific processing proteases;Deubiquitination (Consensus)

Recessive Scores

• pRec: 0.0872

Intolerance Scores

• loftool: 0.988
• rvis_EVS: -0.29
• rvis_percentile_EVS: 33.47

Haploinsufficiency Scores

• pHI: 0.276
• hipred: N
• hipred_score: 0.304
• ghis: 0.479

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.193

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Usp44
• Phenotype: neoplasm; cellular phenotype

Zebrafish Information Network

• Gene name: usp44
• Affected structure: pharyngeal arch cartilage
• Phenotype tag: abnormal
• Phenotype quality: malformed

Gene ontology

• Biological process: cell cycle;protein deubiquitination;proteasome-mediated ubiquitin-dependent protein catabolic process;cell division;regulation of mitotic cell cycle spindle assembly checkpoint;negative regulation of ubiquitin protein ligase activity
• Cellular component: nucleus;nucleoplasm;cytoplasm
• Molecular function: thiol-dependent ubiquitin-specific protease activity;protein binding;zinc ion binding;thiol-dependent ubiquitinyl hydrolase activity