UBFD1

ubiquitin family domain containing 1

Basic information

Region (hg38): 16:23557720-23574389

Links

ENSG00000103353 ∙ NCBI:56061 ∙ ∙ HGNC:30565 ∙ Uniprot:O14562 ∙ 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 UBFD1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the UBFD1 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						0
missense			19			19
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	19	0	0

Variants in UBFD1

This is a list of pathogenic ClinVar variants found in the UBFD1 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-23557958-G-A		not specified	Uncertain significance (May 08, 2024)
16-23557979-G-A		not specified	Uncertain significance (Jan 04, 2022)
16-23557980-C-T		not specified	Uncertain significance (Sep 27, 2021)
16-23557992-C-T		not specified	Uncertain significance (Jan 27, 2022)
16-23558003-C-G		not specified	Uncertain significance (Aug 08, 2022)
16-23558022-G-T		not specified	Uncertain significance (Aug 02, 2023)
16-23558031-C-G		not specified	Uncertain significance (Oct 03, 2022)
16-23558049-C-T		not specified	Uncertain significance (Apr 21, 2022)
16-23558052-C-T		not specified	Uncertain significance (Dec 14, 2021)
16-23558063-T-C		not specified	Uncertain significance (May 30, 2023)
16-23558076-G-A		not specified	Uncertain significance (Dec 28, 2022)
16-23558079-G-A		not specified	Uncertain significance (Aug 12, 2022)
16-23558136-T-G		not specified	Uncertain significance (Jun 21, 2022)
16-23558183-G-A		not specified	Uncertain significance (Nov 07, 2023)
16-23558239-C-G		not specified	Uncertain significance (Apr 18, 2023)
16-23559629-G-A		not specified	Uncertain significance (Nov 13, 2023)
16-23559633-C-G		not specified	Uncertain significance (Mar 25, 2024)
16-23559671-C-G		not specified	Uncertain significance (Apr 24, 2023)
16-23562269-C-A		not specified	Uncertain significance (Jan 23, 2024)
16-23562637-A-G		not specified	Uncertain significance (Aug 30, 2021)
16-23562638-C-T		not specified	Uncertain significance (Jan 11, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
UBFD1	protein_coding	protein_coding	ENST00000395878	7	17319

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.942	0.0576	124789	0	3	124792	0.0000120

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.04	122	159	0.768	0.00000805	1990
Missense in Polyphen		9	25.206	0.35705		336
Synonymous	0.926	58	67.7	0.857	0.00000389	598
Loss of Function	3.14	1	13.4	0.0744	5.73e-7	176

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000579	0.0000579
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00000884	0.00000883
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play a role as NF-kappa-B regulator. {ECO:0000269|PubMed:19285159}.

Recessive Scores

• pRec: 0.109

Intolerance Scores

• loftool: 0.161
• rvis_EVS: 0.01
• rvis_percentile_EVS: 54.95

Haploinsufficiency Scores

• pHI: 0.130
• hipred: Y
• hipred_score: 0.673
• ghis: 0.546

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.453

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ubfd1

Gene ontology

• Molecular function: RNA binding;cadherin binding