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.

• not_specified (77 variants)
• not_provided (6 variants)
• USP44-related_disorder (6 variants)
• Intellectual_disability,_moderate (1 variants)

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. These statistics are base on transcript: NM_000032147.5. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				4	2	6
missense			75	4	3	82
nonsense						0
start loss						0
frameshift			1			1
splice donor/acceptor (+/-2bp)						0
Total	0	0	76	8	5

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