UFC1

ubiquitin-fold modifier conjugating enzyme 1

Basic information

Region (hg38): 1:161152776-161158856

Links

ENSG00000143222 ∙ NCBI:51506 ∙ OMIM:610554 ∙ HGNC:26941 ∙ Uniprot:Q9Y3C8 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• neurodevelopmental disorder with spasticity and poor growth (Strong), mode of inheritance: AR
• neurodevelopmental disorder with spasticity and poor growth (Limited), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Neurodevelopmental disorder with spasticity and poor growth	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Craniofacial; Musculoskeletal; Neurologic	27431290; 29868776

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the UFC1 gene.

• Neurodevelopmental disorder with spasticity and poor growth (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the UFC1 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		1	8			9
nonsense						0
start loss						0
frameshift						0
inframe indel	1					1
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	1	1	8	3	1

Highest pathogenic variant AF is 0.00000657

Variants in UFC1

This is a list of pathogenic ClinVar variants found in the UFC1 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-161152992-G-C			Benign (Feb 01, 2024)
1-161154035-T-A		not specified	Uncertain significance (Apr 01, 2024)
1-161154036-C-G		not specified	Uncertain significance (Aug 15, 2023)
1-161154038-C-T		Neurodevelopmental disorder with spasticity and poor growth	Uncertain significance (Oct 05, 2018)
1-161154045-G-C		UFC1-related disorder	Likely benign (Jun 05, 2019)
1-161154055-G-C		not specified	Uncertain significance (Oct 08, 2024)
1-161154065-G-A		Neurodevelopmental disorder with spasticity and poor growth	Pathogenic (Aug 06, 2018)
1-161156958-GAAC-G		Neurodevelopmental disorder with spasticity and poor growth	Pathogenic (Jun 30, 2022)
1-161156964-C-T			Likely benign (Dec 01, 2023)
1-161156977-A-T		not specified	Uncertain significance (Dec 07, 2021)
1-161156979-C-A		Neurodevelopmental disorder with spasticity and poor growth	Uncertain significance (Aug 23, 2019)
1-161156979-C-T		UFC1-related disorder	Benign (Feb 18, 2019)
1-161156992-C-A		not specified	Uncertain significance (Jun 26, 2024)
1-161157274-A-G		not specified	Uncertain significance (May 08, 2023)
1-161157309-G-A		UFC1-related disorder • not specified	Uncertain significance (Nov 10, 2022)
1-161157678-C-T		Neurodevelopmental disorder with spasticity and poor growth	Likely pathogenic (Mar 17, 2024)
1-161158152-A-G		not specified	Uncertain significance (May 23, 2024)
1-161158153-A-C		not specified	Uncertain significance (Feb 17, 2022)
1-161158165-C-T		not specified	Uncertain significance (May 05, 2023)
1-161158420-A-G			Likely benign (Dec 01, 2022)
1-161158460-G-A		not specified	Uncertain significance (Jan 23, 2023)
1-161158485-A-G		not specified	Likely benign (Dec 10, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
UFC1	protein_coding	protein_coding	ENST00000368003	6	6081

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00362	0.959	125736	0	12	125748	0.0000477

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.234	89	95.4	0.932	0.00000467	1085
Missense in Polyphen		39	43.677	0.89292		497
Synonymous	0.269	34	36.1	0.943	0.00000191	311
Loss of Function	1.82	6	13.1	0.458	7.45e-7	123

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000152	0.000152
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000527	0.0000527
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000653	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: E2-like enzyme which forms an intermediate with UFM1 via a thioester linkage. {ECO:0000269|PubMed:15071506}.

Recessive Scores

• pRec: 0.130

Intolerance Scores

• loftool: 0.658
• rvis_EVS: -0.34
• rvis_percentile_EVS: 30.07

Haploinsufficiency Scores

• pHI: 0.363
• hipred: N
• hipred_score: 0.465
• ghis: 0.620

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.892

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Ufc1

Gene ontology

• Biological process: response to endoplasmic reticulum stress;protein ufmylation;protein K69-linked ufmylation
• Cellular component: extracellular exosome
• Molecular function: protein binding;UFM1 transferase activity