GeneBe

UFSP2

UFM1 specific peptidase 2

Basic information

Region (hg38): 4:185399537-185425979

Previous symbols: [ "C4orf20" ]

Links

ENSG00000109775 ∙ NCBI:55325 ∙ OMIM:611482 ∙ HGNC:25640 ∙ Uniprot:Q9NUQ7 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

  • hip dysplasia, Beukes type (Limited), mode of inheritance: AD
  • hip dysplasia, Beukes type (Supportive), mode of inheritance: AD
  • autosomal recessive non-syndromic intellectual disability (Supportive), mode of inheritance: AR
  • developmental and epileptic encephalopathy 106 (Limited), mode of inheritance: Unknown
  • developmental and epileptic encephalopathy 106 (Limited), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Hip dysplasia, Beukes type; Spondyloepimetaphyseal dysplasia, Di Rocco typeADGeneralGenetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testingMusculoskeletal2389793; 28892125

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the UFSP2 gene.

  • not_specified (50 variants)
  • not_provided (17 variants)
  • Hip_dysplasia,_Beukes_type (7 variants)
  • UFSP2-related_disorder (5 variants)
  • Spondyloepimetaphyseal_dysplasia,_di_rocco_type (5 variants)
  • Developmental_and_epileptic_encephalopathy_106 (5 variants)
  • UFSP2-related_neurodevelopmental_disorder (1 variants)
  • Epileptic_encephalopathy (1 variants)
  • Cerebral_visual_impairment_and_intellectual_disability (1 variants)
  • Developmental_dysplasia_of_the_hip (1 variants)
  • Olivopontocerebellar_hypoplasia (1 variants)
  • Microcephaly (1 variants)
  • Intellectual_disability (1 variants)
  • Severe_global_developmental_delay (1 variants)
  • Focal-onset_seizure (1 variants)
  • Abnormality_of_the_nervous_system (1 variants)
  • Seizure (1 variants)
  • Developmental_and_epileptic_encephalopathy,_1 (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the UFSP2 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000018359.5. 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.

EffectPLPVUSLBBSum
synonymous
5
clinvar
4
clinvar
 9
missense
4
clinvar
3
clinvar
52
clinvar
5
clinvar
1
clinvar
 65
nonsense
0
start loss
0
frameshift
1
clinvar
1
clinvar
1
clinvar
 3
splice donor/acceptor (+/-2bp)
0
Total 5 4 53 10 5

Highest pathogenic variant AF is 0.000071314826

Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
UFSP2protein_codingprotein_codingENST00000264689 1226446
pLI Probability
LOF Intolerant 		pRec Probability
LOF Recessive 		Individuals with
no LOFs 		Individuals with
Homozygous LOFs 		Individuals with
Heterozygous LOFs 		Defined p
0.000003060.9851256860621257480.000247
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.4762352560.9160.00001313070
Missense in Polyphen5880.2360.72287923
Synonymous-0.1249391.51.020.00000501884
Loss of Function2.221325.00.5210.00000112322

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.001110.00111
Ashkenazi Jewish0.0002070.000198
East Asian0.0002870.000272
Finnish0.000.00
European (Non-Finnish)0.0002580.000255
Middle Eastern0.0002870.000272
South Asian0.0001420.000131
Other0.000.00

dbNSFP

Source: dbNSFP

Function
FUNCTION: Thiol protease which recognizes and hydrolyzes the peptide bond at the C-terminal Gly of UFM1, a ubiquitin-like modifier protein bound to a number of target proteins. Does not hydrolyze SUMO1 or ISG15 ubiquitin-like proteins. Through TRIP4 deufmylation may regulate intracellular nuclear receptors transactivation and thereby regulate cell proliferation and differentiation. {ECO:0000269|PubMed:25219498}.;
Disease
DISEASE: Beukes familial hip dysplasia (BFHD) [MIM:142669]: A severe progressive degenerative osteoarthritis of the hip joint with underlying dysplasia confined to that region. Affected individuals are of normal stature and have no associated health problems. {ECO:0000269|PubMed:26428751, ECO:0000269|PubMed:28892125}. Note=The disease is caused by mutations affecting the gene represented in this entry.;

Recessive Scores

pRec
0.107

Intolerance Scores

loftool
0.818
rvis_EVS
-0.03
rvis_percentile_EVS
51.92

Haploinsufficiency Scores

pHI
0.228
hipred
N
hipred_score
0.229
ghis
0.547

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
S
essential_gene_gene_trap
N
gene_indispensability_pred
E
gene_indispensability_score
0.690

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Ufsp2
Phenotype

Gene ontology

Biological process
proteolysis;regulation of intracellular estrogen receptor signaling pathway
Cellular component
nucleus;cytoplasm;endoplasmic reticulum
Molecular function
protein binding;thiolester hydrolase activity;UFM1 hydrolase activity