ANKRD13A

gene
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Also known as NY-REN-25

Summary

ANKRD13A (ankyrin repeat domain 13A, HGNC:21268) is a protein-coding gene on chromosome 12q24.11, encoding Ankyrin repeat domain-containing protein 13A (Q8IZ07). Ubiquitin-binding protein that specifically recognizes and binds ‘Lys-63’-linked ubiquitin.

Enables ubiquitin-modified protein reader activity. Involved in negative regulation of protein localization to endosome and negative regulation of receptor internalization. Located in late endosome; perinuclear region of cytoplasm; and plasma membrane.

Source: NCBI Gene 88455 — RefSeq curated summary.

At a glance

  • GWAS associations: 3
  • Clinical variants (ClinVar): 79 total
  • MANE Select transcript: NM_033121

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:21268
Approved symbolANKRD13A
Nameankyrin repeat domain 13A
Location12q24.11
Locus typegene with protein product
StatusApproved
AliasesNY-REN-25
Ensembl geneENSG00000076513
Ensembl biotypeprotein_coding
OMIM615123
Entrez88455

Gene structure

Transcript identifiers

Ensembl transcripts: 23 — 17 protein_coding, 4 retained_intron, 1 protein_coding_CDS_not_defined, 1 nonsense_mediated_decay

ENST00000261739, ENST00000546476, ENST00000547419, ENST00000547639, ENST00000549826, ENST00000550404, ENST00000551491, ENST00000553025, ENST00000553246, ENST00000553251, ENST00000907288, ENST00000907289, ENST00000907290, ENST00000907291, ENST00000907292, ENST00000907293, ENST00000939845, ENST00000939846, ENST00000939847, ENST00000939848, ENST00000949447, ENST00000949448, ENST00000949449

RefSeq mRNA: 1 — MANE Select: NM_033121 NM_033121

CCDS: CCDS9140

Canonical transcript exons

ENST00000261739 — 15 exons

ExonStartEnd
ENSE00002216022110024046110024112
ENSE00002353288109999430109999784
ENSE00002363473110037359110039763
ENSE00003467475110036261110036328
ENSE00003481323110029478110029635
ENSE00003482636110025742110025823
ENSE00003500653110027705110027766
ENSE00003501883110018345110018488
ENSE00003504807110019139110019328
ENSE00003536566110016388110016433
ENSE00003590833110013125110013249
ENSE00003615964110012005110012137
ENSE00003628799110030645110030758
ENSE00003650611110028512110028642
ENSE00003680952110033797110033957

Expression profiles

Bgee: expression breadth ubiquitous, 261 present calls, max score 98.61.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 29.8470 / max 899.3934, expressed in 1821 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter IDTPM avgSamples expressed
12795829.63561821
1279590.211430

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
upper arm skinUBERON:000426398.61gold quality
amniotic fluidUBERON:000017398.06gold quality
ileal mucosaUBERON:000033197.89gold quality
buccal mucosa cellCL:000233697.70gold quality
adult organismUBERON:000702397.59gold quality
nasal cavity epitheliumUBERON:000538497.53gold quality
spermCL:000001997.39gold quality
bloodUBERON:000017897.16gold quality
upper leg skinUBERON:000426296.88gold quality
palpebral conjunctivaUBERON:000181296.66gold quality
oviduct epitheliumUBERON:000480496.55gold quality
penisUBERON:000098996.50gold quality
parotid glandUBERON:000183196.48gold quality
calcaneal tendonUBERON:000370196.39gold quality
skin of hipUBERON:000155496.31gold quality
trabecular bone tissueUBERON:000248396.10gold quality
secondary oocyteCL:000065596.08gold quality
placentaUBERON:000198796.07gold quality
oral cavityUBERON:000016796.05gold quality
monocyteCL:000057695.99gold quality
leukocyteCL:000073895.93gold quality
tonsilUBERON:000237295.82gold quality
esophagus squamous epitheliumUBERON:000692095.82gold quality
bone marrowUBERON:000237195.70gold quality
vermiform appendixUBERON:000115495.63gold quality
nippleUBERON:000203095.63gold quality
tendonUBERON:000004395.58gold quality
bone elementUBERON:000147495.48gold quality
lymph nodeUBERON:000002995.45gold quality
stromal cell of endometriumCL:000225595.39gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3yes9.71

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

157 targeting ANKRD13A, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-4533100.0069.482758
HSA-MIR-190A-3P100.0080.355520
HSA-MIR-9-5P100.0072.282361
HSA-MIR-5692A100.0074.406850
HSA-LET-7A-3P100.0074.033932
HSA-LET-7B-3P100.0074.083913
HSA-LET-7F-1-3P100.0074.023928
HSA-MIR-98-3P100.0074.083907
HSA-MIR-3613-3P100.0076.367965
HSA-MIR-4455100.0065.481587
HSA-MIR-5011-5P100.0083.465820
HSA-MIR-548C-3P99.9974.017587
HSA-MIR-3667-3P99.9967.171636
HSA-MIR-1213699.9872.815713
HSA-MIR-520D-5P99.9873.344883
HSA-MIR-524-5P99.9873.434882
HSA-MIR-3688-3P99.9772.022834
HSA-MIR-495-3P99.9672.814197
HSA-MIR-568899.9673.234504
HSA-MIR-6825-5P99.9669.813431
HSA-MIR-1236-3P99.9468.041695
HSA-MIR-22-3P99.9368.13917
HSA-MIR-381-3P99.9371.872854
HSA-MIR-6835-3P99.9370.492904
HSA-MIR-539-5P99.9370.302855
HSA-MIR-30099.9271.762856
HSA-MIR-498-3P99.9171.271114
HSA-MIR-548E-5P99.8972.734486
HSA-MIR-6783-3P99.8967.922059
HSA-MIR-1343-3P99.8966.781815

Literature-anchored findings (GeneRIF, showing 6)

  • overexpression of wild-type as well as truncated-mutant Ankrd 13A, 13B and 13D proteins strongly inhibited rapid endocytosis of ubiquitinated EGFR from the surface in EGF-treated cells (PMID:22298428)
  • the microRNA miR-204 promotes both mesenchymal neural crest and lens cell migration and elongation by the direct targeting of the Ankrd13A gene. (PMID:23620728)
  • We validated ANKRD13A as a novel constituent of BCR signalosome and showed that BCR-induced phosphorylation of RAB7A at S72 regulates its association with its effector proteins and with endo-lysosomal compartments. (PMID:26038114)
  • The Ankrd13 family of ubiquitin-interacting motif (UIM)-containing proteins are novel VCP-interacting molecules in the endosome. (PMID:26797118)
  • LncRNA USP30-AS1 promotes the survival of acute myeloid leukemia cells by cis-regulating USP30 and ANKRD13A. (PMID:34694569)
  • ANKRD13a controls early cell-death checkpoint by interacting with RIP1 independent of NF-kappaB. (PMID:34839354)

Cross-species orthologs

5 orthologs

OrganismSymbolGene ID
danio_rerioankrd13aENSDARG00000061901
mus_musculusAnkrd13aENSMUSG00000041870
rattus_norvegicusAnkrd13aENSRNOG00000001204
drosophila_melanogasterCG15118FBGN0034418
caenorhabditis_elegansWBGENE00015978

Paralogs (3): ANKRD13C (ENSG00000118454), ANKRD13D (ENSG00000172932), ANKRD13B (ENSG00000198720)

Protein

Protein identifiers

Ankyrin repeat domain-containing protein 13AQ8IZ07 (reviewed: Q8IZ07)

Alternative names: Protein KE03

All UniProt accessions (6): Q8IZ07, F8W150, H0YIN8, Q3ZTS7, S4R3D2, S4R3U2

UniProt curated annotations — full annotation on UniProt →

Function. Ubiquitin-binding protein that specifically recognizes and binds ‘Lys-63’-linked ubiquitin. Does not bind ‘Lys-48’-linked ubiquitin. Positively regulates the internalization of ligand-activated EGFR by binding to the Ub moiety of ubiquitinated EGFR at the cell membrane.

Subunit / interactions. Interacts (via the UIM 3 and 4 repeats) with EGFR (ubiquitinated); the interaction is direct, inhibited by ANKRD13A monoubiquitination and may regulate EGFR internalization.

Subcellular location. Cell membrane. Late endosome.

Post-translational modifications. Monoubiquitinated, inhibits interaction with ubiquitinated EGFR.

Domain organisation. The UIM repeats 3 and 4 are required for binding to ubiquitinated EGFR and ‘Lys-63’-linked ubiquitin.

RefSeq proteins (1): NP_149112* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR002110Ankyrin_rptRepeat
IPR003903UIM_domConserved_site
IPR021832ANKRD13Family
IPR036770Ankyrin_rpt-contain_sfHomologous_superfamily
IPR055285ANKRD13_CDomain

Pfam: PF11904, PF12796

UniProt features (16 total): mutagenesis site 4, domain 4, repeat 2, sequence conflict 2, modified residue 2, chain 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q8IZ07-F174.080.20

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Post-translational modifications (2): 205, 586

Mutagenesis-validated functional residues (4):

PositionPhenotype
491–495no effect on ’lys-63’-linked ubiquitin binding and interaction with egfr. no effect on ’lys-63’-linked ubiquitin binding
527–531no effect on ’lys-63’-linked ubiquitin binding and interaction with egfr. no effect on ’lys-63’-linked ubiquitin binding
557–561slightly inhibits ’lys-63’-linked ubiquitin binding and strongly inhibits interaction with egfr. no effect on ’lys-63’-l
582–586abolishes ’lys-63’-linked ubiquitin binding and strongly inhibits interaction with egfr. abolishes ’lys-63’-linked ubiqu

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 198 (showing top): MODULE_255, MODULE_317, GOBP_NEGATIVE_REGULATION_OF_ENDOCYTOSIS, GOBP_VESICLE_MEDIATED_TRANSPORT, GOBP_NEGATIVE_REGULATION_OF_PROTEIN_LOCALIZATION, GOBP_REGULATION_OF_VESICLE_MEDIATED_TRANSPORT, MONNIER_POSTRADIATION_TUMOR_ESCAPE_UP, GOBP_NEGATIVE_REGULATION_OF_CELLULAR_COMPONENT_ORGANIZATION, GOBP_NEGATIVE_REGULATION_OF_TRANSPORT, RICKMAN_TUMOR_DIFFERENTIATED_WELL_VS_POORLY_DN, GOBP_REGULATION_OF_RECEPTOR_INTERNALIZATION, GOBP_REGULATION_OF_RECEPTOR_MEDIATED_ENDOCYTOSIS, TGIF_01, ZIC1_01, GOBP_RECEPTOR_INTERNALIZATION

GO Biological Process (2): negative regulation of receptor internalization (GO:0002091), negative regulation of protein localization to endosome (GO:1905667)

GO Molecular Function (2): ubiquitin-modified protein reader activity (GO:0140036), protein binding (GO:0005515)

GO Cellular Component (7): cytoplasm (GO:0005737), late endosome (GO:0005770), plasma membrane (GO:0005886), perinuclear region of cytoplasm (GO:0048471), endosome (GO:0005768), endomembrane system (GO:0012505), membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cellular anatomical structure4
regulation of receptor internalization1
receptor internalization1
negative regulation of receptor-mediated endocytosis1
protein localization to endosome1
negative regulation of protein localization1
regulation of protein localization to endosome1
ubiquitin-like protein reader activity1
binding1
intracellular anatomical structure1
endosome1
membrane1
cell periphery1
cytoplasm1
endomembrane system1
cytoplasmic vesicle1
vacuole1
plasma membrane1

Protein interactions and networks

STRING

790 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
ANKRD13AC12orf43Q96C57532
ANKRD13AVCPP55072513
ANKRD13AUBASH3AP57075477
ANKRD13AGPHA2Q96T91433
ANKRD13AUBXN6Q9BZV1383
ANKRD13AMMABQ96EY8376
ANKRD13AENKD1Q9H0I2366
ANKRD13ATTC39CQ8N584352
ANKRD13APPP2R5BQ15173349
ANKRD13AUBASH3BQ8TF42346
ANKRD13AC2orf69Q8N8R5342
ANKRD13AG3V325G3V325336
ANKRD13ATMEM25Q86YD3336
ANKRD13AGLTPQ9NZD2333
ANKRD13ASMIM14Q96QK8332

IntAct

156 interactions, top by confidence:

ABTypeScore
ENTREP1WWP2psi-mi:“MI:0914”(association)0.850
TSPAN5ADAM10psi-mi:“MI:0914”(association)0.800
ARRDC3WWP2psi-mi:“MI:0914”(association)0.770
CFTRESYT2psi-mi:“MI:0914”(association)0.710
CSNK1G3CSNK1G2psi-mi:“MI:0914”(association)0.640
GNAI3RGS12psi-mi:“MI:0914”(association)0.640
CFTRHAX1psi-mi:“MI:0914”(association)0.610
MS4A10NEDD4psi-mi:“MI:0914”(association)0.590
ASB7POLR3Apsi-mi:“MI:0914”(association)0.530
ZDHHC11APOBpsi-mi:“MI:0914”(association)0.530
RALBDBTpsi-mi:“MI:0914”(association)0.530
ARRDC4WWP2psi-mi:“MI:0914”(association)0.530
LDLRAD4WWP2psi-mi:“MI:0914”(association)0.530
IZUMO1ADCY3psi-mi:“MI:0914”(association)0.530
ZNRF1NMT2psi-mi:“MI:0914”(association)0.530
PI4K2AGABARAPpsi-mi:“MI:0914”(association)0.530
ENTREP3NEDD4psi-mi:“MI:0914”(association)0.530
SLC39A4TMEM120Bpsi-mi:“MI:0914”(association)0.530
TMEM31PSMD11psi-mi:“MI:0914”(association)0.530
CCR6PODXLpsi-mi:“MI:0914”(association)0.530
SCAMP2SCAMP3psi-mi:“MI:0914”(association)0.530
DLK1SCAMP3psi-mi:“MI:0914”(association)0.530

BioGRID (201): ANKRD13A (Two-hybrid), UBC (Reconstituted Complex), ANKRD13A (Affinity Capture-MS), ANKRD13A (Affinity Capture-MS), ANKRD13A (Affinity Capture-MS), ANKRD13A (Affinity Capture-MS), ANKRD13A (Affinity Capture-MS), ANKRD13A (Affinity Capture-MS), ANKRD13A (Affinity Capture-MS), ANKRD13A (Affinity Capture-MS), ANKRD13A (Affinity Capture-MS), ANKRD13A (Affinity Capture-MS), ANKRD13A (Affinity Capture-MS), ANKRD13A (Co-fractionation), ANKRD13A (Affinity Capture-MS)

ESM2 similar proteins: A0A1L8FDW4, A4QP73, A4UMC5, B4NYQ2, B5X0I6, C4R2L0, D4A6D7, O09012, O70525, O74711, P33292, P50542, Q01495, Q1RMV0, Q29RR5, Q2M2R8, Q2TXF0, Q54MD1, Q5AV00, Q5F259, Q5R4F4, Q5U2Y6, Q5ZMQ9, Q6BM14, Q6CT48, Q6DI35, Q6DKK2, Q6FM42, Q6K687, Q6PD24, Q6ZTN6, Q752X0, Q80UP5, Q86YJ7, Q8C437, Q8CC21, Q8IYB4, Q8IZ07, Q8L611, Q920N5

Diamond homologs: A4II29, Q28C34, Q3UX43, Q5F259, Q5U5A6, Q6NRD0, Q6PD24, Q6ZTN6, Q7T3Y0, Q7Z6K4, Q7ZUV0, Q7ZYD9, Q80UP5, Q86WC6, Q86YJ7, Q8IZ07, Q8N6S4, Q91ZA8, Q9D119, Q9TXQ1, Q3V096, P42570, Q0VC93, Q28FJ2, Q4JHE0, Q569N2, Q7Z713

SIGNOR signaling

1 interactions.

AEffectBMechanism
SMURF1unknownANKRD13Aubiquitination

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 202 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:

PathwayPartnersFoldFDR
Amino acid transport across the plasma membrane511.5×8e-03
R-HSA-42536679.7×2e-03
SLC-mediated transmembrane transport156.8×4e-06
Transport of small molecules203.8×7e-05
Neutrophil degranulation183.2×2e-03

GO biological processes:

GO termPartnersFoldFDR
post-Golgi vesicle-mediated transport529.6×6e-04
amino acid transport610.5×5e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance61
Likely benign2
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

2586 predictions. Top by Δscore:

VariantEffectΔscore
12:109999782:CAGG:Cdonor_loss1.0000
12:109999783:AGGT:Adonor_loss1.0000
12:109999784:GGTG:Gdonor_loss1.0000
12:109999785:GT:Gdonor_loss1.0000
12:109999786:T:Adonor_loss1.0000
12:110012003:A:AGacceptor_gain1.0000
12:110012003:A:ATacceptor_loss1.0000
12:110012004:G:GTacceptor_gain1.0000
12:110012004:G:Tacceptor_loss1.0000
12:110012004:GA:Gacceptor_gain1.0000
12:110012004:GAAT:Gacceptor_gain1.0000
12:110012133:GACAG:Gdonor_gain1.0000
12:110012134:ACAG:Adonor_gain1.0000
12:110012135:CAG:Cdonor_gain1.0000
12:110012135:CAGGT:Cdonor_loss1.0000
12:110012136:AG:Adonor_gain1.0000
12:110012137:GG:Gdonor_gain1.0000
12:110012138:G:GGdonor_gain1.0000
12:110013121:CTA:Cacceptor_loss1.0000
12:110013122:TA:Tacceptor_loss1.0000
12:110013123:A:AGacceptor_gain1.0000
12:110013123:AG:Aacceptor_loss1.0000
12:110013124:G:GAacceptor_gain1.0000
12:110013124:GTT:Gacceptor_gain1.0000
12:110013124:GTTTT:Gacceptor_gain1.0000
12:110013217:G:GTdonor_gain1.0000
12:110019131:A:AGacceptor_gain1.0000
12:110019134:A:AGacceptor_gain1.0000
12:110019136:TAG:Tacceptor_loss1.0000
12:110019137:A:AGacceptor_gain1.0000

AlphaMissense

3914 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
12:110012131:T:AW75R1.000
12:110012131:T:CW75R1.000
12:110013136:G:CA81P1.000
12:110016415:T:AW128R1.000
12:110016415:T:CW128R1.000
12:110025781:C:AR281S1.000
12:110025782:G:CR281P1.000
12:110025794:T:CL285P1.000
12:110012048:T:CL47P0.999
12:110013137:C:AA81D0.999
12:110016421:T:CF130L0.999
12:110016422:T:CF130S0.999
12:110016423:C:AF130L0.999
12:110016423:C:GF130L0.999
12:110016427:A:CS132R0.999
12:110016429:C:AS132R0.999
12:110016429:C:GS132R0.999
12:110016430:T:AW133R0.999
12:110016430:T:CW133R0.999
12:110018392:A:GK150E0.999
12:110018394:A:CK150N0.999
12:110018394:A:TK150N0.999
12:110018408:T:CL155P0.999
12:110018410:C:AR156S0.999
12:110018411:G:CR156P0.999
12:110018467:A:CS175R0.999
12:110018469:T:AS175R0.999
12:110018469:T:GS175R0.999
12:110025781:C:GR281G0.999
12:110028569:T:CY335H0.999

dbSNP variants (sampled 300 via entrez): RS1000103581 (12:110009129 T>C), RS1000136168 (12:110008863 C>A,T), RS1000198569 (12:110015291 C>T), RS1000324268 (12:110008909 ATT>A,AT,ATTT), RS1000424766 (12:110008633 C>G), RS1000661736 (12:110007379 T>C), RS1000712311 (12:110007067 C>T), RS1000830052 (12:110037365 C>G), RS1000908268 (12:110003834 C>A), RS1000987362 (12:110013808 T>C), RS1001038671 (12:110030817 G>A), RS1001050760 (12:110022895 T>C), RS1001178337 (12:110029982 C>T), RS1001251619 (12:110029072 T>A), RS1001356161 (12:110014499 T>C)

Disease associations

OMIM: gene MIM:615123 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

3 associations (top):

StudyTraitp-value
GCST001822_15Metabolite levels (MHPG)4.000000e-07
GCST007267_131Systolic blood pressure3.000000e-08
GCST008103_145Bipolar disorder3.000000e-06

EFO canonical traits (2, from GWAS)

EFO IDTrait name
EFO:0005133MHPG measurement
EFO:0006335systolic blood pressure

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
bisphenol Adecreases expression, increases expression, affects cotreatment, increases methylation4
sodium arseniteincreases expression, decreases expression, affects cotreatment, increases abundance2
Valproic Acidaffects expression, increases expression2
aristolochic acid Iincreases expression1
bisphenol Faffects cotreatment, increases expression1
triphenyl phosphateaffects expression1
pirinixic acidincreases expression, affects binding, increases activity1
trichostatin Aaffects expression1
manganese chlorideaffects cotreatment, increases abundance, increases expression1
di-n-butylphosphoric acidaffects expression1
perfluorooctane sulfonic aciddecreases expression1
CGP 52608affects binding, increases reaction1
abrineincreases expression1
bisphenol Saffects cotreatment, decreases expression1
Temozolomidedecreases expression1
Sunitinibincreases expression1
Fulvestrantaffects cotreatment, increases methylation1
Acetaminophenincreases expression1
Arsenicincreases expression, affects cotreatment, increases abundance1
Atrazinedecreases expression1
Caffeinedecreases phosphorylation1
Dexamethasoneaffects cotreatment, increases expression, decreases expression1
Indomethacinaffects cotreatment, increases expression, decreases expression1
Leadaffects expression1
Manganeseincreases expression, affects cotreatment, increases abundance1
Methyl Methanesulfonateincreases expression1
Phthalic Acidsaffects methylation1
Tretinoinincreases expression1
Urethaneincreases expression1
1-Methyl-3-isobutylxanthineaffects cotreatment, increases expression, decreases expression1

Cellosaurus cell lines

1 cell lines: 1 cancer cell line

First 10 cell lines (id-ordered, not curated):

CellosaurusNameCategorySex
CVCL_B1JIAbcam HeLa ANKRD13A KOCancer cell lineFemale

Clinical trials (associated diseases)

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

No linked Atlas pages yet — the cross-entity mesh grows as the corpus expands.