ANKRD53

Summary

ANKRD53 (ankyrin repeat domain 53, HGNC:25691) is a protein-coding gene on chromosome 2p13.3, encoding Ankyrin repeat domain-containing protein 53 (Q8N9V6). Required for normal progression through mitosis.

Involved in mitotic metaphase chromosome alignment; regulation of microtubule cytoskeleton organization; and regulation of mitotic cytokinesis. Located in spindle pole.

Source: NCBI Gene 79998 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 116 total
• MANE Select transcript: NM_001115116

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:25691
Approved symbol	ANKRD53
Name	ankyrin repeat domain 53
Location	2p13.3
Locus type	gene with protein product
Status	Approved
Aliases	FLJ12056, FLJ36160
Ensembl gene	ENSG00000144031
Ensembl biotype	protein_coding
OMIM	617009
Entrez	79998

Gene structure

Transcript identifiers

Ensembl transcripts: 8 — 5 protein_coding, 3 retained_intron

ENST00000272421, ENST00000360589, ENST00000441349, ENST00000457410, ENST00000460927, ENST00000483334, ENST00000496088, ENST00000963655

RefSeq mRNA: 3 — MANE Select: NM_001115116 NM_001115116, NM_001369683, NM_024933

CCDS: CCDS1913, CCDS46321, CCDS92774

Canonical transcript exons

ENST00000360589 — 6 exons

Exon	Start	End
ENSE00001223170	70982577	70982697
ENSE00001223176	70981936	70982100
ENSE00001223194	70979097	70979343
ENSE00001918132	70984611	70985499
ENSE00001952108	70978630	70978815
ENSE00003629400	70979661	70979860

Expression profiles

Bgee: expression breadth ubiquitous, 165 present calls, max score 90.70.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.2952 / max 22.5542, expressed in 152 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
20860	0.2095	108
20859	0.0520	20
20861	0.0337	10

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	90.70	gold quality
right testis	UBERON:0004534	88.82	gold quality
left testis	UBERON:0004533	87.37	gold quality
germinal epithelium of ovary	UBERON:0001304	85.25	gold quality
upper arm skin	UBERON:0004263	84.63	gold quality
testis	UBERON:0000473	84.46	gold quality
left ventricle myocardium	UBERON:0006566	83.05	gold quality
cardiac muscle of right atrium	UBERON:0003379	82.93	gold quality
kidney epithelium	UBERON:0004819	82.64	gold quality
body of pancreas	UBERON:0001150	82.53	gold quality
nasal cavity epithelium	UBERON:0005384	81.96	gold quality
right uterine tube	UBERON:0001302	80.82	gold quality
omental fat pad	UBERON:0010414	78.81	gold quality
peritoneum	UBERON:0002358	78.77	gold quality
left ovary	UBERON:0002119	78.65	gold quality
superficial temporal artery	UBERON:0001614	78.63	gold quality
skeletal muscle tissue of biceps brachii	UBERON:0004502	78.39	gold quality
adipose tissue of abdominal region	UBERON:0007808	78.23	gold quality
right ovary	UBERON:0002118	77.66	gold quality
myocardium	UBERON:0002349	77.52	gold quality
quadriceps femoris	UBERON:0001377	77.01	gold quality
secondary oocyte	CL:0000655	76.84	silver quality
vastus lateralis	UBERON:0001379	76.74	gold quality
mucosa of stomach	UBERON:0001199	75.74	gold quality
biceps brachii	UBERON:0001507	75.59	gold quality
left lobe of thyroid gland	UBERON:0001120	75.09	gold quality
right lobe of thyroid gland	UBERON:0001119	74.81	gold quality
left coronary artery	UBERON:0001626	74.71	gold quality
deltoid	UBERON:0001476	74.70	gold quality
adipose tissue	UBERON:0001013	74.57	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

Experiment	Marker?	Max mean expression
E-ANND-3	no	2.27

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

24 targeting ANKRD53, 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-6798-5P	100.00	65.77	699
HSA-MIR-3692-3P	99.98	70.27	2139
HSA-MIR-6825-5P	99.96	69.81	3431
HSA-MIR-3140-3P	99.88	68.47	2069
HSA-MIR-4492	99.87	68.25	3611
HSA-MIR-4447	99.85	67.81	2900
HSA-MIR-378G	99.71	64.90	1106
HSA-MIR-3714	99.71	70.74	2671
HSA-MIR-3175	99.65	66.30	2031
HSA-MIR-4251	99.40	69.19	3363
HSA-MIR-3678-3P	99.31	67.10	1432
HSA-MIR-6852-5P	99.17	66.69	2073
HSA-MIR-6829-5P	98.86	65.12	1480
HSA-MIR-198	98.70	67.32	920
HSA-MIR-7155-5P	98.65	66.14	1290
HSA-MIR-6776-5P	98.54	67.43	1304
HSA-MIR-3921	97.81	67.45	1431
HSA-MIR-4741	97.69	64.14	883
HSA-MIR-4675	97.69	64.82	774
HSA-MIR-4653-5P	97.22	67.72	1429
HSA-MIR-505-5P	97.01	65.54	778
HSA-MIR-597-5P	96.82	67.57	732
HSA-MIR-4296	96.35	63.55	1233
HSA-MIR-6796-5P	95.37	66.08	1120

Literature-anchored findings (GeneRIF, showing 1)

• Thus, ANKRD53 is recruited to the mitotic spindle by DDA3 and acts as a regulator of spindle dynamics and cytokinesis. (PMID:26820536)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	ankrd53	ENSDARG00000098445
mus_musculus	Ankrd53	ENSMUSG00000014747
rattus_norvegicus	Ankrd53	ENSRNOG00000021402

Protein

Protein identifiers

Ankyrin repeat domain-containing protein 53 — Q8N9V6 (reviewed: Q8N9V6)

All UniProt accessions (3): Q8N9V6, C9JQK2, C9JZ61

UniProt curated annotations — full annotation on UniProt →

Function. Required for normal progression through mitosis. Involved in chromosome alignment and cytokinesis via regulation of microtubules polymerization.

Subunit / interactions. Interacts with PSRC1; recruited by PSRC1 to the spindle during mitosis.

Subcellular location. Cytoplasm. Cytoskeleton. Spindle. Spindle pole.

Post-translational modifications. Phosphorylated during mitosis.

Isoforms (2)

UniProt ID	Names	Canonical?
Q8N9V6-1	1	yes
Q8N9V6-2	2

RefSeq proteins (3): NP_001108588, NP_001356612, NP_079209 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR002110	Ankyrin_rpt	Repeat
IPR036770	Ankyrin_rpt-contain_sf	Homologous_superfamily
IPR042335	ANKRD53	Family

Pfam: PF00023, PF12796

UniProt features (19 total): sequence variant 5, compositionally biased region 4, repeat 3, region of interest 3, splice variant 2, chain 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8N9V6-F1	62.41	0.16

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 86 (showing top): GSE18804_BRAIN_VS_COLON_TUMORAL_MACROPHAGE_DN, GOBP_MITOTIC_CYTOKINESIS, GOBP_CHROMOSOME_ORGANIZATION, GOBP_REGULATION_OF_PROTEIN_POLYMERIZATION, GOBP_REGULATION_OF_MICROTUBULE_BASED_PROCESS, GOBP_CHROMOSOME_LOCALIZATION, GOBP_POSITIVE_REGULATION_OF_ORGANELLE_ORGANIZATION, GOBP_REGULATION_OF_CELLULAR_COMPONENT_BIOGENESIS, GOBP_POSITIVE_REGULATION_OF_CELLULAR_COMPONENT_BIOGENESIS, GOBP_POSITIVE_REGULATION_OF_MICROTUBULE_POLYMERIZATION_OR_DEPOLYMERIZATION, GOBP_ORGANELLE_FISSION, GOBP_REGULATION_OF_MICROTUBULE_POLYMERIZATION, GOBP_CYTOKINESIS, GOBP_REGULATION_OF_SPINDLE_ORGANIZATION, GOBP_REGULATION_OF_CELL_CYCLE

GO Biological Process (5): mitotic metaphase chromosome alignment (GO:0007080), positive regulation of microtubule polymerization (GO:0031116), cell division (GO:0051301), regulation of mitotic spindle organization (GO:0060236), regulation of mitotic cytokinesis (GO:1902412)

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

GO Cellular Component (4): spindle pole (GO:0000922), spindle (GO:0005819), cytoplasm (GO:0005737), cytoskeleton (GO:0005856)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	2
intracellular membraneless organelle	2
mitotic sister chromatid segregation	1
mitotic cell cycle	1
metaphase chromosome alignment	1
mitotic cell cycle process	1
positive regulation of microtubule polymerization or depolymerization	1
regulation of microtubule polymerization	1
positive regulation of protein polymerization	1
microtubule polymerization	1
positive regulation of supramolecular fiber organization	1
cellular process	1
mitotic spindle organization	1
regulation of spindle organization	1
mitotic cytokinesis	1
regulation of cytokinesis	1
binding	1
spindle	1
microtubule cytoskeleton	1
intracellular anatomical structure	1

Protein interactions and networks

STRING

591 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ANKRD53	TDRD10	Q5VZ19	572
ANKRD53	ZNF154	Q13106	543
ANKRD53	PLEKHS1	Q5SXH7	447
ANKRD53	TAF11	Q15544	433
ANKRD53	CLXN	Q9HAE3	419
ANKRD53	PRAC2	D3DTV9	419
ANKRD53	ZNF177	Q13360	395
ANKRD53	LVRN	Q6Q4G3	364
ANKRD53	TMEM132C	Q8N3T6	349
ANKRD53	AGAP5	A6NIR3	348
ANKRD53	RIMBP2	O15034	336
ANKRD53	HOXD9	P28356	328
ANKRD53	MOB3B	Q86TA1	324
ANKRD53	RNF220	Q5VTB9	322
ANKRD53	VAX2	Q9UIW0	317

IntAct

2 interactions, top by confidence:

A	B	Type	Score
LZTR1	ANKRD53	psi-mi:“MI:0915”(physical association)	0.370

BioGRID (4): ANKRD53 (Affinity Capture-MS), ANKRD53 (Two-hybrid), GLYCTK (Two-hybrid), ANKRD53 (Two-hybrid)

ESM2 similar proteins: A0A1L8HBI7, A0A1L8HJK9, A0A1L8HTT5, A4QP16, A6NP61, B2RVL6, C0SPG1, C3VD30, K7SGN7, O54880, P56163, Q1XFL1, Q29RJ0, Q2KI52, Q32L09, Q3V0J4, Q4R2Y2, Q4R739, Q58D79, Q5RAK6, Q5TKR9, Q5VWQ0, Q6PDK8, Q768S4, Q7T3T8, Q7T3T9, Q80T69, Q86US8, Q86Y01, Q8AW93, Q8BMD7, Q8BRB7, Q8BZ21, Q8CAK3, Q8CDN1, Q8HXK7, Q8K3Y6, Q8N2G6, Q8N9V6, Q8TE76

Diamond homologs: P25631, Q18297, Q4R739, Q8N9V6, Q9J4Z4, Q9UU77, A0A084B9Z8, A4II29, A6NGH8, G3I6Z6, G5EDE9, O00221, O15084, O35516, O54910, O73630, O89019, O90760, P01125, P01126, P15307, P15330, P16236, P19838, P20749, P25799, P25963, P31695, P46531, P51509, P51510, P53356, P98149, P98150, P98152, Q00653, Q01201, Q01705, Q04206, Q04207

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	100
Likely benign	11
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1093 predictions. Top by Δscore:

Variant	Effect	Δscore
2:70979342:AGGTA:A	donor_loss	1.0000
2:70979343:GGTA:G	donor_loss	1.0000
2:70979344:G:GA	donor_loss	1.0000
2:70979344:G:GG	donor_gain	1.0000
2:70979857:ATGC:A	donor_gain	1.0000
2:70979859:GC:G	donor_gain	1.0000
2:70979860:CGT:C	donor_loss	1.0000
2:70979861:G:GG	donor_gain	1.0000
2:70979862:T:G	donor_loss	1.0000
2:70981903:T:TA	acceptor_gain	1.0000
2:70981910:A:AG	acceptor_gain	1.0000
2:70981911:T:G	acceptor_gain	1.0000
2:70981916:A:AG	acceptor_gain	1.0000
2:70981916:ACT:A	acceptor_gain	1.0000
2:70981916:ACTG:A	acceptor_gain	1.0000
2:70981917:C:G	acceptor_gain	1.0000
2:70981918:T:A	acceptor_gain	1.0000
2:70981919:G:A	acceptor_gain	1.0000
2:70981934:A:AG	acceptor_gain	1.0000
2:70981935:G:GA	acceptor_gain	1.0000
2:70982105:GAGT:G	donor_gain	1.0000
2:70982107:GT:G	donor_gain	1.0000
2:70982685:GAT:G	donor_gain	1.0000
2:70982687:T:G	donor_gain	1.0000
2:70982687:T:TG	donor_gain	1.0000
2:70982691:G:GG	donor_gain	1.0000
2:70982698:G:GG	donor_gain	1.0000
2:70979342:AG:A	donor_gain	0.9900
2:70979343:GG:G	donor_gain	0.9900
2:70979349:GTCT:G	donor_gain	0.9900

AlphaMissense

3487 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
2:70979664:T:C	F141L	0.985
2:70979666:C:A	F141L	0.985
2:70979666:C:G	F141L	0.985
2:70982582:T:C	L263S	0.983
2:70982578:T:C	F262L	0.981
2:70982580:C:A	F262L	0.981
2:70982580:C:G	F262L	0.981
2:70982071:C:G	C251W	0.977
2:70982070:G:A	C251Y	0.974
2:70979686:C:A	A148D	0.973
2:70982598:G:C	W268C	0.973
2:70982598:G:T	W268C	0.973
2:70979290:T:A	W122R	0.972
2:70979290:T:C	W122R	0.972
2:70979683:C:A	A147D	0.972
2:70984974:T:C	F423L	0.972
2:70984976:C:A	F423L	0.972
2:70984976:C:G	F423L	0.972
2:70979773:C:A	P177H	0.968
2:70982069:T:C	C251R	0.968
2:70979833:T:C	L197P	0.966
2:70982596:T:A	W268R	0.965
2:70982596:T:C	W268R	0.965
2:70979736:T:C	F165L	0.964
2:70979738:T:A	F165L	0.964
2:70979738:T:G	F165L	0.964
2:70982058:C:A	P247H	0.962
2:70982586:G:C	K264N	0.962
2:70982586:G:T	K264N	0.962
2:70979279:G:T	G118V	0.961

dbSNP variants (sampled 300 via entrez): RS1000188860 (2:70985812 G>A), RS1000461676 (2:70980354 G>C), RS1001736976 (2:70979145 C>T), RS1002104412 (2:70979342 A>C,T), RS1002120408 (2:70983933 C>T), RS1002192378 (2:70983640 A>G), RS1004105657 (2:70978146 T>A,C), RS1004621168 (2:70982567 T>C), RS1004691405 (2:70983970 C>T), RS1004993530 (2:70982921 A>G), RS1006247524 (2:70981279 G>A), RS1006652499 (2:70979742 G>A), RS1006689297 (2:70985726 T>A), RS1006733099 (2:70980971 C>T), RS1006762760 (2:70985485 C>G,T)

Disease associations

OMIM: gene MIM:617009 | 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

17 total (human), top 17 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Benzo(a)pyrene	affects methylation, decreases methylation, increases expression	2
aristolochic acid I	increases expression	1
bisphenol A	decreases methylation	1
ethyl-p-hydroxybenzoate	increases expression	1
butyraldehyde	increases expression	1
abrine	increases expression	1
bisphenol S	affects cotreatment, increases expression	1
Resveratrol	decreases expression, affects cotreatment	1
Acetaminophen	decreases expression	1
Dexamethasone	affects cotreatment, increases expression	1
Endosulfan	increases expression	1
Indomethacin	affects cotreatment, increases expression	1
Plant Extracts	affects cotreatment, decreases expression	1
Tobacco Smoke Pollution	decreases expression	1
Valproic Acid	affects expression	1
1-Methyl-3-isobutylxanthine	affects cotreatment, increases expression	1
Asbestos, Serpentine	increases methylation	1

Clinical trials (associated diseases)

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