USP16

ubiquitin specific peptidase 16, the group of Ubiquitin specific peptidases

Basic information

Region (hg38): 21:29024629-29054488

Links

ENSG00000156256 ∙ ∙ OMIM:604735 ∙ HGNC:12614 ∙ Uniprot:Q9Y5T5 ∙ 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 USP16 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the USP16 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	1
missense			43	1		44
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	43	1	2

Variants in USP16

This is a list of pathogenic ClinVar variants found in the USP16 region.

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

Position	Type	Phenotype	Significance	ClinVar
21-29027936-G-A		not specified	Uncertain significance (Aug 01, 2024)
21-29027962-T-G		not specified	Uncertain significance (May 30, 2024)
21-29030603-T-A		not specified	Uncertain significance (Jun 02, 2023)
21-29030702-G-A		not specified	Uncertain significance (Nov 21, 2022)
21-29030726-A-G		not specified	Uncertain significance (Jan 04, 2024)
21-29034837-G-A		not specified	Uncertain significance (Sep 24, 2024)
21-29034892-G-C		not specified	Uncertain significance (Dec 04, 2024)
21-29036362-A-G		not specified	Uncertain significance (Oct 20, 2024)
21-29036368-A-C		not specified	Uncertain significance (Jan 17, 2024)
21-29037330-G-A		not specified	Uncertain significance (Oct 06, 2021)
21-29037365-A-G		not specified	Uncertain significance (Sep 01, 2021)
21-29037384-C-T		not specified	Uncertain significance (Sep 06, 2022)
21-29037428-T-A		not specified	Uncertain significance (Aug 12, 2022)
21-29038357-T-C		not specified	Uncertain significance (Dec 08, 2023)
21-29038411-C-T		not specified	Uncertain significance (Jan 30, 2024)
21-29038417-A-T		not specified	Uncertain significance (Feb 06, 2023)
21-29039046-T-G			Benign (Mar 27, 2018)
21-29039053-C-G		not specified	Uncertain significance (Nov 18, 2022)
21-29039089-A-T		not specified	Uncertain significance (Jun 26, 2023)
21-29039126-C-T		not specified	Uncertain significance (Jul 27, 2024)
21-29039501-A-G		not specified	Uncertain significance (Aug 21, 2024)
21-29039507-A-G		not specified	Uncertain significance (Jan 08, 2024)
21-29039531-G-A		not specified	Uncertain significance (Aug 02, 2021)
21-29040640-G-C		not specified	Uncertain significance (Aug 02, 2021)
21-29040668-A-T		not specified	Uncertain significance (Mar 19, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
USP16	protein_coding	protein_coding	ENST00000334352	17	29860

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.85e-9	0.998	125653	0	95	125748	0.000378

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.350	399	419	0.952	0.0000205	5505
Missense in Polyphen		137	177.44	0.77208		2405
Synonymous	1.29	126	146	0.865	0.00000747	1430
Loss of Function	2.83	21	40.4	0.520	0.00000186	559

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00103	0.00103
Ashkenazi Jewish	0.00	0.00
East Asian	0.000115	0.000109
Finnish	0.0000467	0.0000462
European (Non-Finnish)	0.000322	0.000316
Middle Eastern	0.000115	0.000109
South Asian	0.000824	0.000752
Other	0.000326	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Specifically deubiquitinates 'Lys-120' of histone H2A (H2AK119Ub), a specific tag for epigenetic transcriptional repression, thereby acting as a coactivator. Deubiquitination of histone H2A is a prerequisite for subsequent phosphorylation at 'Ser-11' of histone H3 (H3S10ph), and is required for chromosome segregation when cells enter into mitosis. In resting B- and T- lymphocytes, phosphorylation by AURKB leads to enhance its activity, thereby maintaining transcription in resting lymphocytes. Regulates Hox gene expression via histone H2A deubiquitination. Prefers nucleosomal substrates. Does not deubiquitinate histone H2B. {ECO:0000255|HAMAP-Rule:MF_03062, ECO:0000269|PubMed:10077596, ECO:0000269|PubMed:17914355}.
• Disease: DISEASE: Note=A chromosomal aberration involving USP16 is a cause of Chronic myelomonocytic leukemia. Inversion inv(21) (q21;q22) with RUNX1/AML1.
• Pathway: Post-translational protein modification;Metabolism of proteins;Ub-specific processing proteases;Deubiquitination (Consensus)

Recessive Scores

• pRec: 0.108

Intolerance Scores

• loftool: 0.981
• rvis_EVS: -0.09
• rvis_percentile_EVS: 47.06

Haploinsufficiency Scores

• pHI: 0.235
• hipred: Y
• hipred_score: 0.637
• ghis: 0.586

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.621

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Usp16
• 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: mitotic cell cycle;regulation of transcription by RNA polymerase II;ubiquitin-dependent protein catabolic process;cellular response to DNA damage stimulus;histone deubiquitination;protein deubiquitination;monoubiquitinated histone H2A deubiquitination;positive regulation of transcription, DNA-templated;positive regulation of translational elongation;positive regulation of transcription by RNA polymerase II;protein homotetramerization;cell division;regulation of cell cycle;histone H2A K63-linked deubiquitination;mitotic nuclear division
• Cellular component: nucleus;nucleoplasm;cytoplasm
• Molecular function: transcription coactivator activity;cysteine-type endopeptidase activity;thiol-dependent ubiquitin-specific protease activity;zinc ion binding;thiol-dependent ubiquitinyl hydrolase activity;histone binding;ubiquitin binding