UFD1

ubiquitin recognition factor in ER associated degradation 1

Basic information

Region (hg38): 22:19449910-19479202

Previous symbols: [ "UFD1L" ]

Links

ENSG00000070010 ∙ NCBI:7353 ∙ OMIM:601754 ∙ HGNC:12520 ∙ Uniprot:Q92890 ∙ 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 UFD1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the UFD1 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				3	1	4
missense			8			8
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding					12	12
Total	0	0	8	3	13

Variants in UFD1

This is a list of pathogenic ClinVar variants found in the UFD1 region.

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

Position	Type	Phenotype	Significance	ClinVar
22-19450678-T-C		not specified	Uncertain significance (Apr 22, 2024)
22-19450679-T-C		UFD1-related disorder	Likely benign (Mar 07, 2019)
22-19450723-C-T		not specified	Uncertain significance (May 03, 2023)
22-19450821-G-A			Benign (May 20, 2021)
22-19450839-A-G			Benign (May 19, 2021)
22-19454808-T-G		not specified	Uncertain significance (Feb 10, 2022)
22-19455648-C-T			Benign (May 24, 2021)
22-19455755-G-A		not specified	Uncertain significance (Jun 06, 2023)
22-19455788-G-C			Benign (May 20, 2021)
22-19456408-G-T			Benign (May 16, 2021)
22-19456608-A-G			Likely benign (Jun 06, 2018)
22-19456658-G-A			Benign (May 17, 2021)
22-19456857-G-A		not specified	Uncertain significance (Dec 15, 2021)
22-19458119-C-T		not specified	Uncertain significance (Dec 08, 2023)
22-19467853-C-T			Benign (May 17, 2021)
22-19467952-C-T		not specified	Uncertain significance (Jan 30, 2024)
22-19467953-G-A			Likely benign (Jun 16, 2018)
22-19467974-G-A		UFD1-related disorder	Benign (Dec 31, 2019)
22-19468082-G-A			Benign (May 16, 2021)
22-19471634-A-G			Benign (May 17, 2021)
22-19474943-C-G			Benign (May 15, 2021)
22-19475094-A-C		not specified	Uncertain significance (Dec 20, 2022)
22-19475574-A-G		not specified	Uncertain significance (Jan 16, 2024)
22-19478862-G-A			Benign (May 17, 2021)
22-19478942-C-G			Benign (May 25, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
UFD1	protein_coding	protein_coding	ENST00000263202	12	29306

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.996	0.00362	125745	0	2	125747	0.00000795

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.71	80	183	0.437	0.0000103	2027
Missense in Polyphen		11	60.372	0.1822		744
Synonymous	1.02	58	68.8	0.843	0.00000420	566
Loss of Function	4.04	1	21.0	0.0477	0.00000117	233

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00000879	0.00000879
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Essential component of the ubiquitin-dependent proteolytic pathway which degrades ubiquitin fusion proteins. The ternary complex containing UFD1, VCP and NPLOC4 binds ubiquitinated proteins and is necessary for the export of misfolded proteins from the ER to the cytoplasm, where they are degraded by the proteasome. The NPLOC4-UFD1-VCP complex regulates spindle disassembly at the end of mitosis and is necessary for the formation of a closed nuclear envelope. It may be involved in the development of some ectoderm-derived structures (By similarity). Acts as a negative regulator of type I interferon production via the complex formed with VCP and NPLOC4, which binds to DDX58/RIG-I and recruits RNF125 to promote ubiquitination and degradation of DDX58/RIG-I (PubMed:26471729). {ECO:0000250|UniProtKB:Q9ES53, ECO:0000269|PubMed:26471729}.
• Pathway: Protein processing in endoplasmic reticulum - Homo sapiens (human);DNA Repair;Post-translational protein modification;Metabolism of proteins;Ub-specific processing proteases;Deubiquitination;Translesion Synthesis by POLH;Translesion synthesis by Y family DNA polymerases bypasses lesions on DNA template;DNA Damage Bypass (Consensus)

Recessive Scores

• pRec: 0.160

Intolerance Scores

• rvis_EVS: 0.06
• rvis_percentile_EVS: 58.26

Haploinsufficiency Scores

• pHI: 0.447
• hipred: Y
• hipred_score: 0.775
• ghis: 0.543

Essentials

• essential_gene_gene_trap: E

Mouse Genome Informatics

• Gene name: Ufd1
• Phenotype: normal phenotype

Zebrafish Information Network

• Gene name: ufd1l
• Affected structure: anatomical system
• Phenotype tag: abnormal
• Phenotype quality: quality

Gene ontology

• Biological process: skeletal system development;ubiquitin-dependent protein catabolic process;protein deubiquitination;retrograde protein transport, ER to cytosol;negative regulation of type I interferon production;negative regulation of RIG-I signaling pathway;proteasome-mediated ubiquitin-dependent protein catabolic process;error-free translesion synthesis;ER-associated misfolded protein catabolic process
• Cellular component: nucleus;nucleoplasm;endoplasmic reticulum;cytosol;VCP-NPL4-UFD1 AAA ATPase complex;UFD1-NPL4 complex
• Molecular function: thiol-dependent ubiquitin-specific protease activity;signaling receptor binding;protein binding;K48-linked polyubiquitin modification-dependent protein binding;protein-containing complex binding;ATPase binding