UFL1

UFM1 specific ligase 1

Basic information

Region (hg38): 6:96521595-96555276

Previous symbols: [ "KIAA0776" ]

Links

ENSG00000014123NCBI:23376OMIM:613372HGNC:23039Uniprot:O94874AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the UFL1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the UFL1 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
clinvar
1
missense
57
clinvar
1
clinvar
2
clinvar
60
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
0
non coding
0
Total 0 0 57 1 3

Variants in UFL1

This is a list of pathogenic ClinVar variants found in the UFL1 region.

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

Position Type Phenotype Significance ClinVar
6-96521893-A-G not specified Uncertain significance (Nov 20, 2024)3465551
6-96521899-G-C not specified Uncertain significance (Apr 07, 2023)2511328
6-96521908-C-G not specified Uncertain significance (Feb 07, 2023)2481634
6-96523174-G-A not specified Uncertain significance (Dec 19, 2022)2337540
6-96523206-A-C not specified Uncertain significance (May 06, 2024)3330793
6-96523219-C-T not specified Uncertain significance (Sep 06, 2024)3465554
6-96524387-G-C not specified Uncertain significance (Dec 17, 2023)3186022
6-96525313-T-G not specified Uncertain significance (May 07, 2024)3330799
6-96525349-A-G not specified Uncertain significance (Aug 14, 2023)2600496
6-96526326-A-T not specified Uncertain significance (Aug 16, 2022)2352821
6-96526383-C-G not specified Uncertain significance (Jun 09, 2022)2364693
6-96526404-C-T not specified Uncertain significance (Oct 12, 2021)2411093
6-96528572-C-T not specified Uncertain significance (Apr 22, 2024)3330797
6-96528583-G-A not specified Uncertain significance (Dec 27, 2023)3186024
6-96528593-A-G not specified Uncertain significance (Sep 04, 2024)3465552
6-96528607-C-T not specified Uncertain significance (Jan 02, 2024)2301011
6-96536270-G-A not specified Uncertain significance (Apr 13, 2022)2214834
6-96536334-A-G not specified Uncertain significance (Jun 11, 2021)2232930
6-96537381-T-G not specified Uncertain significance (Jul 09, 2021)2393380
6-96537452-T-C not specified Uncertain significance (Jan 02, 2024)3186025
6-96537458-T-G not specified Uncertain significance (Feb 27, 2023)2489847
6-96537470-G-A not specified Uncertain significance (Dec 18, 2023)3186026
6-96537513-A-C not specified Uncertain significance (Mar 02, 2023)2465854
6-96537529-G-A not specified Uncertain significance (Sep 13, 2023)2623830
6-96538660-A-C not specified Uncertain significance (Aug 01, 2022)2406440

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
UFL1protein_codingprotein_codingENST00000369278 1933682
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
1.17e-120.97812562501231257480.000489
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.1893934040.9740.00002025193
Missense in Polyphen87102.340.850111336
Synonymous-0.04261431421.000.000007111476
Loss of Function2.382642.80.6080.00000227538

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.001030.00101
Ashkenazi Jewish0.0001010.0000992
East Asian0.0004640.000435
Finnish0.0001920.000185
European (Non-Finnish)0.0006710.000642
Middle Eastern0.0004640.000435
South Asian0.0003800.000359
Other0.0003580.000326

dbNSFP

Source: dbNSFP

Function
FUNCTION: E3 protein ligase that mediates ufmylation, the covalent attachment of the ubiquitin-like modifier UFM1 to substrate proteins, a post-translational modification on lysine residues of proteins that may play a crucial role in a number of cellular processes. Mediates DDRGK1 ufmylation and may regulate the proteasomal degradation of DDRGK1 and CDK5RAP3 thereby modulating NF-kappa-B signaling (PubMed:20018847, PubMed:20164180, PubMed:20228063, PubMed:25219498). May also through TRIP4 ufmylation play a role in nuclear receptors-mediated transcription (PubMed:25219498). May play a role in the unfolded protein response, mediating the ufmylation of multiple proteins in response to endoplasmic reticulum stress (PubMed:23152784). {ECO:0000269|PubMed:20018847, ECO:0000269|PubMed:20164180, ECO:0000269|PubMed:20228063, ECO:0000269|PubMed:23152784, ECO:0000269|PubMed:25219498}.;
Pathway
Immune System;Adaptive Immune System;Antigen processing: Ubiquitination & Proteasome degradation;Class I MHC mediated antigen processing & presentation (Consensus)

Recessive Scores

pRec
0.104

Intolerance Scores

loftool
rvis_EVS
-0.78
rvis_percentile_EVS
13.05

Haploinsufficiency Scores

pHI
0.757
hipred
Y
hipred_score
0.614
ghis
0.655

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
S
essential_gene_gene_trap
N
gene_indispensability_pred
N
gene_indispensability_score
0.114

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Ufl1
Phenotype
immune system phenotype; embryo phenotype; liver/biliary system phenotype; hematopoietic system 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); adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); homeostasis/metabolism phenotype; cellular phenotype; growth/size/body region phenotype;

Gene ontology

Biological process
osteoblast differentiation;positive regulation of cell population proliferation;negative regulation of protein ubiquitination;negative regulation of NF-kappaB transcription factor activity;regulation of proteasomal ubiquitin-dependent protein catabolic process;regulation of protein localization;regulation of intracellular estrogen receptor signaling pathway;response to endoplasmic reticulum stress;negative regulation of apoptotic process;positive regulation of glial cell proliferation;protein ufmylation;response to L-glutamate;protein K69-linked ufmylation
Cellular component
cytoplasm;endoplasmic reticulum;endoplasmic reticulum membrane;cytosol;membrane;protein-containing complex;neuron projection
Molecular function
protein binding;UFM1 transferase activity