ANKUB1

Summary

ANKUB1 (ankyrin repeat and ubiquitin domain containing 1, HGNC:29642) is a protein-coding gene on chromosome 3q25.1, encoding Protein ANKUB1 (A6NFN9).

At a glance

• GWAS associations: 2
• Clinical variants (ClinVar): 86 total
• MANE Select transcript: NM_001144960

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:29642
Approved symbol	ANKUB1
Name	ankyrin repeat and ubiquitin domain containing 1
Location	3q25.1
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000206199
Ensembl biotype	protein_coding
Entrez	389161

Gene structure

Transcript identifiers

Ensembl transcripts: 9 — 5 protein_coding_CDS_not_defined, 2 protein_coding, 1 retained_intron, 1 nonsense_mediated_decay

ENST00000446160, ENST00000462519, ENST00000462561, ENST00000473672, ENST00000474224, ENST00000474404, ENST00000481585, ENST00000484019, ENST00000497728

RefSeq mRNA: 3 — MANE Select: NM_001144960 NM_001144960, NM_001315505, NM_001315506

CCDS: CCDS82857

Canonical transcript exons

ENST00000446160 — 6 exons

Exon	Start	End
ENSE00001494525	149780239	149780455
ENSE00001662287	149761100	149761613
ENSE00003617971	149767157	149768095
ENSE00003669441	149770560	149770674
ENSE00003678250	149790781	149790924
ENSE00003803912	149792277	149792554

Expression profiles

Bgee: expression breadth ubiquitous, 137 present calls, max score 88.94.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.2377 / max 62.0131, expressed in 53 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter ID	TPM avg	Samples expressed
45061	0.1053	34
45062	0.0620	22
45059	0.0430	21
45060	0.0275	12

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
olfactory segment of nasal mucosa	UBERON:0005386	88.94	gold quality
right uterine tube	UBERON:0001302	82.68	gold quality
bronchial epithelial cell	CL:0002328	81.71	gold quality
bronchus	UBERON:0002185	80.40	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	74.46	gold quality
oviduct epithelium	UBERON:0004804	73.46	gold quality
buccal mucosa cell	CL:0002336	72.86	silver quality
mucosa of paranasal sinus	UBERON:0005030	67.91	silver quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	67.59	gold quality
nasal cavity mucosa	UBERON:0001826	67.11	gold quality
fallopian tube	UBERON:0003889	66.42	gold quality
calcaneal tendon	UBERON:0003701	66.32	gold quality
bone marrow cell	CL:0002092	64.78	gold quality
right lung	UBERON:0002167	62.81	gold quality
nasal cavity epithelium	UBERON:0005384	61.78	gold quality
corpus callosum	UBERON:0002336	61.74	gold quality
sperm	CL:0000019	60.14	gold quality
lower lobe of lung	UBERON:0008949	60.04	silver quality
leukocyte	CL:0000738	58.78	gold quality
monocyte	CL:0000576	58.58	gold quality
tibial nerve	UBERON:0001323	57.04	gold quality
left testis	UBERON:0004533	56.96	gold quality
tendon	UBERON:0000043	56.92	gold quality
right testis	UBERON:0004534	56.78	gold quality
granulocyte	CL:0000094	56.20	gold quality
testis	UBERON:0000473	55.80	gold quality
upper leg skin	UBERON:0004262	55.11	silver quality
adrenal tissue	UBERON:0018303	55.09	gold quality
colonic epithelium	UBERON:0000397	54.78	silver quality
endothelial cell	CL:0000115	54.71	gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 2.

Experiment	Marker?	Max mean expression
E-ANND-3	yes	8.33
E-CURD-112	yes	3.72

Regulation

Is transcription factor: no

Literature-anchored findings (GeneRIF, showing 1)

• Novel frameshift mutations of ANKUB1, GLI3, and TAS2R3 associated with polysyndactyly in a Chinese family. (PMID:32253825)

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Ankub1	ENSMUSG00000074591
rattus_norvegicus	Ankub1	ENSRNOG00000070034

Paralogs (10): UBL4A (ENSG00000102178), NEDD8 (ENSG00000129559), RPS27A (ENSG00000143947), UBC (ENSG00000150991), UBB (ENSG00000170315), ZFAND4 (ENSG00000172671), UBL4B (ENSG00000186150), ISG15 (ENSG00000187608), UBD (ENSG00000213886), UBA52 (ENSG00000221983)

Protein

Protein identifiers

Protein ANKUB1 — A6NFN9 (reviewed: A6NFN9)

Alternative names: Ankyrin repeat and ubiquitin domain-containing 1

All UniProt accessions (2): A6NFN9, C9JND2

Isoforms (3)

UniProt ID	Names	Canonical?
A6NFN9-2	2	yes
A6NFN9-1	1
A6NFN9-3	3

RefSeq proteins (3): NP_001138432, NP_001302434, NP_001302435 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR000626	Ubiquitin-like_dom	Domain
IPR002110	Ankyrin_rpt	Repeat
IPR029071	Ubiquitin-like_domsf	Homologous_superfamily
IPR036770	Ankyrin_rpt-contain_sf	Homologous_superfamily
IPR042788	ANKUB1	Family

Pfam: PF13637

UniProt features (11 total): sequence conflict 4, splice variant 3, sequence variant 3, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-A6NFN9-F1	74.58	0.49

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 46 (showing top): GSE45365_NK_CELL_VS_CD8A_DC_MCMV_INFECTION_UP, DODD_NASOPHARYNGEAL_CARCINOMA_DN, chr3q25, HMGA1_TARGET_GENES, ID1_TARGET_GENES, MAFG_TARGET_GENES, ZNF22_TARGET_GENES, MIR15A_5P, MIR195_5P, MIR15B_5P, MIR16_5P, MIR6838_5P, MIR424_5P, MIR497_5P, MIR4760_3P

GO Biological Process (0):

GO Molecular Function (1): protein binding (GO:0005515)

GO Cellular Component (0):

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
binding	1

Protein interactions and networks

STRING

192 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ANKUB1	COMMD2	Q86X83	618
ANKUB1	LRRC71	Q8N4P6	561
ANKUB1	ANKRD66	B4E2M5	545
ANKUB1	FAM216B	Q8N7L0	536
ANKUB1	CFC1B	P0CG36	507
ANKUB1	DYNLT5	Q8N7M0	495
ANKUB1	HOATZ	Q6PI97	468
ANKUB1	WWTR1	Q9GZV5	454
ANKUB1	CALHM2	Q9HA72	443
ANKUB1	CFAP70	Q5T0N1	442
ANKUB1	DAW1	Q8N136	438
ANKUB1	TAS2R3	Q9NYW6	430
ANKUB1	TMEM255A	Q5JRV8	429
ANKUB1	PPP1R17	O96001	429
ANKUB1	TMC5	Q6UXY8	425

IntAct

0 interactions, top by confidence:

BioGRID (2): ANKUB1 (Affinity Capture-RNA), ANKUB1 (Affinity Capture-RNA)

ESM2 similar proteins: A0A2R8VHF7, A0JM23, A2QRA0, A4IIA7, A4IIV4, A6NFN9, A6NHR9, A7MBF6, F4IG73, F4JSE7, O17482, O95876, P12540, P21784, P34089, P38899, P55895, P56696, Q08AW4, Q0D2D7, Q12789, Q13829, Q28DC9, Q2WGJ8, Q3E7Y5, Q3UUE9, Q4R907, Q4VXA5, Q5BK83, Q5EA90, Q5F476, Q5HZS2, Q5M9F0, Q5RAX4, Q5RBH4, Q5RD21, Q6AYL6, Q6DGA7, Q6PIY5, Q70XZ2

Diamond homologs: A6NFN9, Q3UUE9

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	75
Likely benign	6
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

3755 predictions. Top by Δscore:

Variant	Effect	Δscore
3:149846136:TAGCA:T	donor_gain	1.0000
3:149846137:AGCA:A	donor_gain	1.0000
3:149846137:AGCAG:A	donor_loss	1.0000
3:149846138:GCA:G	donor_gain	1.0000
3:149846138:GCAG:G	donor_gain	1.0000
3:149846139:CA:C	donor_gain	1.0000
3:149846141:G:GG	donor_gain	1.0000
3:149846142:T:A	donor_loss	1.0000
3:149846143:A:AG	donor_loss	1.0000
3:149846144:AGTA:A	donor_loss	1.0000
3:149852514:A:AG	acceptor_gain	1.0000
3:149852515:G:GA	acceptor_gain	1.0000
3:149852515:GT:G	acceptor_gain	1.0000
3:149852515:GTAT:G	acceptor_gain	1.0000
3:149852515:GTATA:G	acceptor_gain	1.0000
3:149872023:TTTCA:T	acceptor_loss	1.0000
3:149872024:TTCA:T	acceptor_loss	1.0000
3:149872025:TCA:T	acceptor_loss	1.0000
3:149872026:CAGG:C	acceptor_loss	1.0000
3:149872027:AG:A	acceptor_gain	1.0000
3:149872028:GG:G	acceptor_gain	1.0000
3:149872150:TAAAG:T	donor_loss	1.0000
3:149872151:AAAGG:A	donor_loss	1.0000
3:149872152:AAGGT:A	donor_loss	1.0000
3:149872153:AGGTA:A	donor_loss	1.0000
3:149872154:GGTAT:G	donor_loss	1.0000
3:149872155:G:GC	donor_loss	1.0000
3:149872156:T:A	donor_loss	1.0000
3:149895463:T:TA	acceptor_gain	1.0000
3:149895468:TGCA:T	acceptor_loss	1.0000

AlphaMissense

3558 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
3:149770642:A:G	W162R	0.985
3:149770642:A:T	W162R	0.985
3:149770651:A:G	W159R	0.983
3:149770651:A:T	W159R	0.983
3:149768089:C:A	Q191H	0.982
3:149768089:C:G	Q191H	0.982
3:149790869:A:G	L49S	0.979
3:149780315:A:C	S125R	0.978
3:149780315:A:T	S125R	0.978
3:149780317:T:G	S125R	0.978
3:149767922:G:T	A247D	0.976
3:149767920:C:G	A248P	0.968
3:149768063:G:T	A200D	0.968
3:149770621:A:G	C169R	0.968
3:149770649:C:A	W159C	0.963
3:149770649:C:G	W159C	0.963
3:149767923:C:G	A247P	0.962
3:149790837:A:G	W60R	0.962
3:149790837:A:T	W60R	0.962
3:149770632:A:G	F165S	0.960
3:149790792:A:G	C75R	0.960
3:149767987:G:C	H225Q	0.956
3:149767987:G:T	H225Q	0.956
3:149767885:A:C	F259L	0.953
3:149767885:A:T	F259L	0.953
3:149767887:A:G	F259L	0.953
3:149767988:T:C	H225R	0.953
3:149768034:A:G	W210R	0.953
3:149768034:A:T	W210R	0.953
3:149780322:G:C	P123R	0.953

dbSNP variants (sampled 300 via entrez): RS1000165825 (3:149765497 C>T), RS1000179838 (3:149761212 C>T), RS1000413547 (3:149794081 C>G), RS1000493144 (3:149766970 G>A,C), RS1000529793 (3:149771214 T>C), RS1000636921 (3:149766599 A>G), RS1000743268 (3:149770297 C>T), RS1000782437 (3:149794109 G>C,T), RS1000834356 (3:149771594 T>C), RS1001011900 (3:149763962 A>G), RS1001017719 (3:149782415 T>A), RS1001174532 (3:149793570 G>A), RS1001271250 (3:149776263 C>CT), RS1001448685 (3:149765022 C>T), RS1001730205 (3:149780951 T>A)

Disease associations

OMIM: gene `` | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

2 associations (top):

Study	Trait	p-value
GCST006629_91	Pulse pressure	9.000000e-11
GCST010142_40	Fish- and plant-related diet	1.000000e-08

EFO canonical traits (2, from GWAS)

EFO ID	Trait name
EFO:0005763	pulse pressure measurement
EFO:0008111	diet measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

12 total (human), top 12 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Benzo(a)pyrene	increases mutagenesis, affects methylation	2
2-methyl-4-isothiazolin-3-one	increases expression	1
jinfukang	affects cotreatment, increases expression	1
theaflavin-3,3’-digallate	affects expression	1
Air Pollutants	increases abundance, increases expression	1
Cisplatin	affects cotreatment, increases expression	1
Estradiol	affects cotreatment, decreases expression	1
Ivermectin	decreases expression	1
Methotrexate	increases expression	1
Smoke	increases abundance, increases expression	1
Tobacco Smoke Pollution	decreases expression	1
Aflatoxin B1	increases methylation	1

Clinical trials (associated diseases)

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