UFL1
Basic information
Region (hg38): 6:96521595-96555276
Previous symbols: [ "KIAA0776" ]
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
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 | |||||
missense | 57 | 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) | ||
6-96521899-G-C | not specified | Uncertain significance (Apr 07, 2023) | ||
6-96521908-C-G | not specified | Uncertain significance (Feb 07, 2023) | ||
6-96523174-G-A | not specified | Uncertain significance (Dec 19, 2022) | ||
6-96523206-A-C | not specified | Uncertain significance (May 06, 2024) | ||
6-96523219-C-T | not specified | Uncertain significance (Sep 06, 2024) | ||
6-96524387-G-C | not specified | Uncertain significance (Dec 17, 2023) | ||
6-96525313-T-G | not specified | Uncertain significance (May 07, 2024) | ||
6-96525349-A-G | not specified | Uncertain significance (Aug 14, 2023) | ||
6-96526326-A-T | not specified | Uncertain significance (Aug 16, 2022) | ||
6-96526383-C-G | not specified | Uncertain significance (Jun 09, 2022) | ||
6-96526404-C-T | not specified | Uncertain significance (Oct 12, 2021) | ||
6-96528572-C-T | not specified | Uncertain significance (Apr 22, 2024) | ||
6-96528583-G-A | not specified | Uncertain significance (Dec 27, 2023) | ||
6-96528593-A-G | not specified | Uncertain significance (Sep 04, 2024) | ||
6-96528607-C-T | not specified | Uncertain significance (Jan 02, 2024) | ||
6-96536270-G-A | not specified | Uncertain significance (Apr 13, 2022) | ||
6-96536334-A-G | not specified | Uncertain significance (Jun 11, 2021) | ||
6-96537381-T-G | not specified | Uncertain significance (Jul 09, 2021) | ||
6-96537452-T-C | not specified | Uncertain significance (Jan 02, 2024) | ||
6-96537458-T-G | not specified | Uncertain significance (Feb 27, 2023) | ||
6-96537470-G-A | not specified | Uncertain significance (Dec 18, 2023) | ||
6-96537513-A-C | not specified | Uncertain significance (Mar 02, 2023) | ||
6-96537529-G-A | not specified | Uncertain significance (Sep 13, 2023) | ||
6-96538660-A-C | not specified | Uncertain significance (Aug 01, 2022) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
UFL1 | protein_coding | protein_coding | ENST00000369278 | 19 | 33682 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
1.17e-12 | 0.978 | 125625 | 0 | 123 | 125748 | 0.000489 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 0.189 | 393 | 404 | 0.974 | 0.0000202 | 5193 |
Missense in Polyphen | 87 | 102.34 | 0.85011 | 1336 | ||
Synonymous | -0.0426 | 143 | 142 | 1.00 | 0.00000711 | 1476 |
Loss of Function | 2.38 | 26 | 42.8 | 0.608 | 0.00000227 | 538 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.00103 | 0.00101 |
Ashkenazi Jewish | 0.000101 | 0.0000992 |
East Asian | 0.000464 | 0.000435 |
Finnish | 0.000192 | 0.000185 |
European (Non-Finnish) | 0.000671 | 0.000642 |
Middle Eastern | 0.000464 | 0.000435 |
South Asian | 0.000380 | 0.000359 |
Other | 0.000358 | 0.000326 |
dbNSFP
Source:
- 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
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
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