UFL1

UFM1 specific ligase 1

Basic information

Region (hg38): 6:96521595-96555276

Previous symbols: [ "KIAA0776" ]

Links

ENSG00000014123 ∙ NCBI:23376 ∙ OMIM:613372 ∙ HGNC:23039 ∙ Uniprot:O94874 ∙ 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 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	1
missense			57	1	2	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)
6-96523157-G-T		not specified	Uncertain significance (Feb 04, 2025)
6-96523174-G-A		not specified	Uncertain significance (Feb 14, 2025)
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)
6-96526340-G-T		not specified	Uncertain significance (Dec 28, 2024)
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)
6-96536253-A-G		not specified	Uncertain significance (Mar 07, 2025)
6-96536270-G-A		not specified	Uncertain significance (Apr 13, 2022)
6-96536334-A-G		not specified	Uncertain significance (Jun 11, 2021)
6-96536370-T-C		not specified	Uncertain significance (Jan 07, 2025)
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)

GnomAD

Source: gnomAD

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: 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

• 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