USP27X

ubiquitin specific peptidase 27 X-linked, the group of Ubiquitin specific peptidases

Basic information

Region (hg38): X:49879484-49882558

Links

ENSG00000273820

∙ NCBI:389856 ∙ OMIM:300975 ∙ HGNC:13486 ∙ Uniprot:A6NNY8 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

intellectual disability, X-linked 105 (Strong), mode of inheritance: XL
non-syndromic X-linked intellectual disability (Supportive), mode of inheritance: XL
X-linked intellectual disability (Limited), mode of inheritance: XL
intellectual disability, X-linked 105 (Strong), mode of inheritance: XL
intellectual disability, X-linked 105 (Strong), mode of inheritance: XL

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Intellectual developmental disorder, X-linked 105	XL	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Neurologic	25644381

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the USP27X gene.

not_provided (29 variants)
Intellectual_disability,_X-linked_105 (18 variants)
Inborn_genetic_diseases (17 variants)
not_specified (5 variants)
USP27X-related_disorder (3 variants)
Neurodevelopmental_disorder (1 variants)
Intellectual_disability (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the USP27X gene is commonly pathogenic or not. These statistics are base on transcript: NM_001145073.3. 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	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous				8 clinvar	2 clinvar	10
missense	1 clinvar	2 clinvar	43 clinvar	2 clinvar	1 clinvar	49
nonsense		2 clinvar				2
start loss						0
frameshift	2 clinvar	3 clinvar	2 clinvar			7
splice donor/acceptor (+/-2bp)						0
Total	3	7	45	10	3

Loading clinvar variants...

GnomAD

Source: gnomAD

dbNSFP

Source: dbNSFP

Function: FUNCTION: Deubiquitinase that can reduce the levels of BCL2L11/BIM ubiquitination and stabilize BCL2L11 in response to the RAF-MAPK- degradation signal. By acting on BCL2L11 levels, may counteract the anti-apoptotic effects of MAPK activity. {ECO:0000250|UniProtKB:Q8CEG8}.;
Disease: DISEASE: Mental retardation, X-linked 105 (MRX105) [MIM:300984]: A form of mental retardation, a disorder characterized by significantly below average general intellectual functioning associated with impairments in adaptive behavior and manifested during the developmental period. Intellectual deficiency is the only primary symptom of non-syndromic X-linked mental retardation, while syndromic mental retardation presents with associated physical, neurological and/or psychiatric manifestations. {ECO:0000269|PubMed:25644381}. Note=The disease is caused by mutations affecting the gene represented in this entry.;

Recessive Scores

pRec: 0.110

Haploinsufficiency Scores

pHI: 0.446
hipred: N
hipred_score: 0.368
ghis

Essentials

essential_gene_CRISPR
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.539

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Usp27x
Phenotype

Gene ontology

Biological process: ubiquitin-dependent protein catabolic process;protein deubiquitination;positive regulation of apoptotic process;protein stabilization;protein K63-linked deubiquitination;protein K48-linked deubiquitination
Cellular component: nucleus;cytosol
Molecular function: thiol-dependent ubiquitin-specific protease activity;Lys63-specific deubiquitinase activity;Lys48-specific deubiquitinase activity