UBFD1

Summary

UBFD1 (ubiquitin family domain containing 1, HGNC:30565) is a protein-coding gene on chromosome 16p12.2, encoding Ubiquitin domain-containing protein UBFD1 (O14562). May play a role as NF-kappa-B regulator.

Enables RNA binding activity and cadherin binding activity.

Source: NCBI Gene 56061 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 59 total
• MANE Select transcript: NM_019116

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:30565
Approved symbol	UBFD1
Name	ubiquitin family domain containing 1
Location	16p12.2
Locus type	gene with protein product
Status	Approved
Aliases	FLJ42145, FLJ38870, UBPH
Ensembl gene	ENSG00000103353
Ensembl biotype	protein_coding
OMIM	621059
Entrez	56061

Gene structure

Transcript identifiers

Ensembl transcripts: 14 — 7 protein_coding, 4 retained_intron, 3 protein_coding_CDS_not_defined

ENST00000395878, ENST00000563366, ENST00000564106, ENST00000565634, ENST00000566136, ENST00000566669, ENST00000567212, ENST00000567264, ENST00000569919, ENST00000571064, ENST00000926412, ENST00000926413, ENST00000926414, ENST00000941976

RefSeq mRNA: 1 — MANE Select: NM_019116 NM_019116

CCDS: CCDS10613

Canonical transcript exons

ENST00000395878 — 7 exons

Exon	Start	End
ENSE00001291859	23570480	23574389
ENSE00002594446	23557727	23557767
ENSE00003489570	23562206	23562271
ENSE00003521367	23559468	23559676
ENSE00003587216	23562625	23562730
ENSE00003612157	23557950	23558279
ENSE00003641344	23566987	23567069

Expression profiles

Bgee: expression breadth ubiquitous, 265 present calls, max score 98.38.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 35.3649 / max 440.6453, expressed in 1813 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
153159	34.1385	1813
153158	1.2264	764

Top tissues by expression

283 total, by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
secondary oocyte	CL:0000655	98.38	gold quality
gastrocnemius	UBERON:0001388	97.14	gold quality
oocyte	CL:0000023	96.84	gold quality
adrenal tissue	UBERON:0018303	96.79	gold quality
muscle of leg	UBERON:0001383	96.54	gold quality
hindlimb stylopod muscle	UBERON:0004252	94.75	gold quality
cerebellar vermis	UBERON:0004720	93.66	gold quality
muscle organ	UBERON:0001630	93.33	gold quality
cortical plate	UBERON:0005343	92.65	gold quality
skeletal muscle tissue of rectus abdominis	UBERON:0004511	92.55	gold quality
stromal cell of endometrium	CL:0002255	92.41	gold quality
right testis	UBERON:0004534	92.12	gold quality
ganglionic eminence	UBERON:0004023	92.10	gold quality
left testis	UBERON:0004533	91.91	gold quality
middle temporal gyrus	UBERON:0002771	91.16	gold quality
cerebellar cortex	UBERON:0002129	91.08	gold quality
cerebellar hemisphere	UBERON:0002245	91.07	gold quality
islet of Langerhans	UBERON:0000006	91.04	gold quality
tibialis anterior	UBERON:0001385	90.88	gold quality
pons	UBERON:0000988	90.85	gold quality
ventricular zone	UBERON:0003053	90.83	gold quality
testis	UBERON:0000473	90.69	gold quality
right hemisphere of cerebellum	UBERON:0014890	90.60	gold quality
right atrium auricular region	UBERON:0006631	90.56	gold quality
right adrenal gland cortex	UBERON:0035827	90.31	gold quality
cerebellum	UBERON:0002037	90.29	gold quality
right adrenal gland	UBERON:0001233	90.28	gold quality
left adrenal gland	UBERON:0001234	90.21	gold quality
adrenal gland	UBERON:0002369	89.96	gold quality
heart left ventricle	UBERON:0002084	89.94	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-ANND-3	yes	4.45

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

197 targeting UBFD1, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-4673	100.00	66.64	1490
HSA-LET-7A-3P	100.00	74.03	3932
HSA-LET-7B-3P	100.00	74.08	3913
HSA-LET-7F-1-3P	100.00	74.02	3928
HSA-MIR-98-3P	100.00	74.08	3907
HSA-MIR-29A-3P	100.00	73.11	1835
HSA-MIR-9-5P	100.00	72.28	2361
HSA-MIR-29B-3P	100.00	73.18	1833
HSA-MIR-29C-3P	100.00	73.15	1833
HSA-MIR-513A-5P	100.00	69.77	2465
HSA-MIR-4747-5P	100.00	67.90	2681
HSA-MIR-5196-5P	100.00	67.98	2761
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-150-5P	99.99	66.69	1976
HSA-MIR-4645-5P	99.98	65.81	1284
HSA-MIR-3692-3P	99.98	70.27	2139
HSA-MIR-27A-3P	99.98	72.13	2955
HSA-MIR-27B-3P	99.98	72.13	2955
HSA-MIR-9985	99.98	72.11	2939
HSA-MIR-548AN	99.97	70.91	2817
HSA-MIR-507	99.97	70.11	1915
HSA-MIR-3148	99.97	75.06	6478
HSA-MIR-590-3P	99.96	74.34	6478
HSA-MIR-4666A-3P	99.96	71.71	3434
HSA-MIR-3658	99.96	73.87	4379
HSA-MIR-548AA	99.96	70.64	3753
HSA-MIR-548AP-3P	99.96	70.64	3753
HSA-MIR-548T-3P	99.96	70.64	3753
HSA-MIR-557	99.96	70.01	1640
HSA-MIR-570-3P	99.96	72.41	4910

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	ubfd1	ENSDARG00000102827
mus_musculus	Ubfd1	ENSMUSG00000030870
rattus_norvegicus	Ubfd1	ENSRNOG00000018243

Protein

Protein identifiers

Ubiquitin domain-containing protein UBFD1 — O14562 (reviewed: O14562)

Alternative names: Ubiquitin-binding protein homolog

All UniProt accessions (3): O14562, H3BRL3, H3BUM8

UniProt curated annotations — full annotation on UniProt →

Function. May play a role as NF-kappa-B regulator.

Subunit / interactions. Binds polyubiquitin.

RefSeq proteins (1): NP_061989* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR000626	Ubiquitin-like_dom	Domain
IPR019954	Ubiquitin_CS	Conserved_site
IPR029071	Ubiquitin-like_domsf	Homologous_superfamily
IPR039120	UBFD1	Family
IPR057455	UBFD1_C	Domain

Pfam: PF00240, PF25343

UniProt features (8 total): compositionally biased region 4, region of interest 2, chain 1, domain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-O14562-F1	72.07	0.32

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 186 (showing top): TGCTGCT_MIR15A_MIR16_MIR15B_MIR195_MIR424_MIR497, TTGGGAG_MIR150, BLALOCK_ALZHEIMERS_DISEASE_UP, SCHAEFFER_PROSTATE_DEVELOPMENT_6HR_DN, DODD_NASOPHARYNGEAL_CARCINOMA_UP, CCAGGTT_MIR490, AGTCAGC_MIR345, IVANOVA_HEMATOPOIESIS_INTERMEDIATE_PROGENITOR, CHANDRAN_METASTASIS_UP, ATGTTTC_MIR494, NUYTTEN_EZH2_TARGETS_DN, chr16p12, WANG_TUMOR_INVASIVENESS_UP, GCACTTT_MIR175P_MIR20A_MIR106A_MIR106B_MIR20B_MIR519D, GAZDA_DIAMOND_BLACKFAN_ANEMIA_ERYTHROID_DN

GO Biological Process (0):

GO Molecular Function (3): RNA binding (GO:0003723), cadherin binding (GO:0045296), protein binding (GO:0005515)

GO Cellular Component (0):

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
nucleic acid binding	1
cell adhesion molecule binding	1
binding	1

Protein interactions and networks

STRING

1502 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
UBFD1	PSMD10	O75832	654
UBFD1	DCTN5	Q9BTE1	603
UBFD1	PSMD3	O43242	567
UBFD1	NDUFAB1	O14561	510
UBFD1	EARS2	Q5JPH6	492
UBFD1	NUDCD3	Q8IVD9	489
UBFD1	ZFAND6	Q6FIF0	486
UBFD1	TTC17	Q96AE7	485
UBFD1	N4BP1	O75113	475
UBFD1	FBXW4	P57775	461
UBFD1	SLC39A9	Q9NUM3	440
UBFD1	ZNF185	O15231	429
UBFD1	ERN2	Q76MJ5	422
UBFD1	STUM	Q69YW2	403
UBFD1	CALCOCO2	Q13137	403

IntAct

11 interactions, top by confidence:

A	B	Type	Score
FSD1	UBFD1	psi-mi:“MI:0914”(association)	0.530
KRIT1	UBFD1	psi-mi:“MI:0914”(association)	0.350
PSMC4	PSMD1	psi-mi:“MI:0914”(association)	0.350
VENTX	UBA6	psi-mi:“MI:0914”(association)	0.350
SEM1	PSMD9	psi-mi:“MI:0914”(association)	0.350
CDH1	ESYT2	psi-mi:“MI:2364”(proximity)	0.270
FHIP2A	MED19	psi-mi:“MI:2364”(proximity)	0.270
SWSAP1	NACA	psi-mi:“MI:2364”(proximity)	0.270

BioGRID (78): UBFD1 (Affinity Capture-MS), UBFD1 (Affinity Capture-MS), EIF4E (Co-fractionation), UBFD1 (Proximity Label-MS), UBFD1 (Affinity Capture-MS), UBFD1 (Affinity Capture-MS), UBFD1 (Affinity Capture-MS), UBFD1 (Affinity Capture-MS), UBFD1 (Affinity Capture-MS), UBFD1 (Affinity Capture-MS), UBFD1 (Affinity Capture-MS), UBFD1 (Proximity Label-MS), UBFD1 (Affinity Capture-MS), UBFD1 (Affinity Capture-MS), UBFD1 (Proximity Label-MS)

ESM2 similar proteins: A0A4X1TB62, A5D7H2, A7MB16, F1Q8X5, O14562, O35841, O42611, P0C606, P23116, P54198, P55884, P58405, P79987, Q13033, Q13112, Q14152, Q15542, Q1JU68, Q4G061, Q569Z1, Q5E9L7, Q5KU39, Q5R644, Q5R660, Q5R7U7, Q61666, Q676U5, Q6NYU2, Q6PCR7, Q8BHL5, Q8C092, Q8CBY8, Q8JZQ9, Q8QFR2, Q8VHE0, Q91W86, Q96ES7, Q96KG9, Q9BZZ5, Q9D0N7

Diamond homologs: O14562, Q78JW9, Q92353

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 14 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

Pathway	Partners	Fold	FDR
Antigen processing: Ubiquitination & Proteasome degradation	5	18.6×	7e-05

Disease & clinical

Clinical variants and AI predictions

ClinVar

59 variants total. Per-class counts are floors (≥ shown; pagination cap):

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	51
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1167 predictions. Top by Δscore:

Variant	Effect	Δscore
16:23558276:ACAGG:A	donor_loss	1.0000
16:23558277:CAGGT:C	donor_loss	1.0000
16:23558278:AGGT:A	donor_loss	1.0000
16:23558279:GGTAA:G	donor_loss	1.0000
16:23558280:GT:G	donor_loss	1.0000
16:23559466:A:G	acceptor_gain	1.0000
16:23559673:GAAA:G	donor_gain	1.0000
16:23559674:A:T	donor_gain	1.0000
16:23559674:AAA:A	donor_gain	1.0000
16:23559674:AAAG:A	donor_loss	1.0000
16:23559675:AA:A	donor_gain	1.0000
16:23559675:AAG:A	donor_loss	1.0000
16:23559676:AGT:A	donor_loss	1.0000
16:23559677:G:GG	donor_gain	1.0000
16:23559677:GT:G	donor_loss	1.0000
16:23559678:TGAG:T	donor_loss	1.0000
16:23562614:C:A	acceptor_gain	1.0000
16:23562726:TAAAG:T	donor_loss	1.0000
16:23562727:AAAGG:A	donor_loss	1.0000
16:23562728:AAGG:A	donor_loss	1.0000
16:23562729:AGGTA:A	donor_loss	1.0000
16:23562730:GGTA:G	donor_loss	1.0000
16:23562732:T:A	donor_loss	1.0000
16:23558280:G:GG	donor_gain	0.9900
16:23558281:T:A	donor_loss	0.9900
16:23559441:A:AG	acceptor_gain	0.9900
16:23559442:C:G	acceptor_gain	0.9900
16:23559455:A:AG	acceptor_gain	0.9900
16:23559456:C:G	acceptor_gain	0.9900
16:23559465:AAGGT:A	acceptor_loss	0.9900

AlphaMissense

2025 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
16:23558198:T:A	W92R	1.000
16:23558198:T:C	W92R	1.000
16:23558204:A:G	K94E	1.000
16:23558253:T:C	L110P	1.000
16:23558257:A:C	K111N	1.000
16:23558257:A:T	K111N	1.000
16:23559471:T:C	L120P	1.000
16:23559486:A:C	Q125P	1.000
16:23559487:G:C	Q125H	1.000
16:23559487:G:T	Q125H	1.000
16:23559488:A:C	K126Q	1.000
16:23559488:A:G	K126E	1.000
16:23559489:A:T	K126I	1.000
16:23559490:A:C	K126N	1.000
16:23559490:A:T	K126N	1.000
16:23559492:T:A	V127D	1.000
16:23559495:T:A	M128K	1.000
16:23559495:T:C	M128T	1.000
16:23559495:T:G	M128R	1.000
16:23559500:A:G	K130E	1.000
16:23559502:G:C	K130N	1.000
16:23559502:G:T	K130N	1.000
16:23559503:G:A	G131R	1.000
16:23559503:G:C	G131R	1.000
16:23559504:G:A	G131E	1.000
16:23559510:T:A	V133D	1.000
16:23559528:T:C	L139S	1.000
16:23559557:A:G	K149E	1.000
16:23559559:G:C	K149N	1.000
16:23559559:G:T	K149N	1.000

dbSNP variants (sampled 300 via entrez): RS1000010172 (16:23571460 C>G), RS1000062590 (16:23571757 A>G), RS1000618336 (16:23565682 C>A,T), RS1000742441 (16:23560535 G>C), RS1001014889 (16:23569916 G>A,C), RS1001068716 (16:23570147 G>A), RS1001147757 (16:23572087 G>A), RS1001173741 (16:23569899 T>C), RS1001271390 (16:23572313 T>C), RS1001720402 (16:23565290 C>T), RS1001892463 (16:23559922 C>T), RS1001903798 (16:23560264 T>C), RS1002052886 (16:23565916 C>G,T), RS1002180821 (16:23571271 G>A), RS1002500499 (16:23566099 G>T)

Disease associations

OMIM: gene MIM:621059 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

37 total (human), top 30 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Air Pollutants	affects cotreatment, increases abundance, increases oxidation, decreases expression	2
Nickel	increases expression	2
Valproic Acid	affects expression, increases methylation	2
Copper Sulfate	decreases expression, increases expression	2
aristolochic acid I	increases expression	1
bisphenol F	increases expression	1
triphenyl phosphate	affects expression	1
alpha-pinene	affects cotreatment, increases oxidation, increases abundance	1
bisphenol A	increases expression	1
tris(1,3-dichloro-2-propyl)phosphate	increases expression	1
cobaltous chloride	increases expression	1
potassium chromate(VI)	affects cotreatment, increases expression	1
methacrylaldehyde	affects cotreatment, increases oxidation, increases abundance	1
diallyl trisulfide	increases expression	1
beta-methylcholine	affects expression	1
epigallocatechin gallate	affects cotreatment, increases expression	1
CGP 52608	affects binding, increases reaction	1
Acrolein	affects cotreatment, increases oxidation, increases abundance	1
Atrazine	increases expression	1
Benzo(a)pyrene	affects methylation	1
Cadmium	increases abundance, increases expression	1
Copper	affects binding, decreases expression	1
Disulfiram	affects binding, decreases expression	1
Doxorubicin	affects expression	1
Enzyme Inhibitors	decreases activity, increases O-linked glycosylation	1
Formaldehyde	increases expression	1
Hydrogen Peroxide	increases expression, affects cotreatment	1
Lead	affects splicing	1
Methyl Methanesulfonate	increases expression	1
Ozone	increases oxidation, increases abundance, affects cotreatment	1

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.