ANKRD13B

Summary

ANKRD13B (ankyrin repeat domain 13B, HGNC:26363) is a protein-coding gene on chromosome 17q11.2, encoding Ankyrin repeat domain-containing protein 13B (Q86YJ7). Ubiquitin-binding protein that specifically recognizes and binds ‘Lys-63’-linked ubiquitin.

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

Source: NCBI Gene 124930 — RefSeq curated summary.

At a glance

• GWAS associations: 6
• Clinical variants (ClinVar): 82 total
• MANE Select transcript: NM_152345

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:26363
Approved symbol	ANKRD13B
Name	ankyrin repeat domain 13B
Location	17q11.2
Locus type	gene with protein product
Status	Approved
Aliases	FLJ25555
Ensembl gene	ENSG00000198720
Ensembl biotype	protein_coding
OMIM	615124
Entrez	124930

Gene structure

Transcript identifiers

Ensembl transcripts: 13 — 8 protein_coding, 4 retained_intron, 1 nonsense_mediated_decay

ENST00000394859, ENST00000487527, ENST00000488766, ENST00000493506, ENST00000578811, ENST00000578943, ENST00000579719, ENST00000583728, ENST00000614878, ENST00000930025, ENST00000930026, ENST00000967256, ENST00000967257

RefSeq mRNA: 1 — MANE Select: NM_152345 NM_152345

CCDS: CCDS11251

Canonical transcript exons

ENST00000394859 — 15 exons

Exon	Start	End
ENSE00003459450	29612402	29612554
ENSE00003505897	29607742	29607877
ENSE00003523530	29609355	29609421
ENSE00003529568	29611579	29611643
ENSE00003533707	29612116	29612273
ENSE00003549584	29608195	29608240
ENSE00003556317	29607986	29608110
ENSE00003572089	29608851	29608994
ENSE00003588296	29610685	29610766
ENSE00003631196	29609086	29609275
ENSE00003644895	29612652	29612815
ENSE00003666329	29613354	29614761
ENSE00003685619	29612887	29612963
ENSE00003693032	29611876	29612006
ENSE00003848255	29593132	29593735

Expression profiles

Bgee: expression breadth ubiquitous, 220 present calls, max score 97.19.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 8.3513 / max 145.0359, expressed in 1567 samples.

FANTOM5 promoters (5 alternative TSS)

Promoter ID	TPM avg	Samples expressed
160111	6.4946	1507
160113	0.7557	368
160112	0.5863	323
160110	0.3736	182
160114	0.1411	39

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
right hemisphere of cerebellum	UBERON:0014890	97.19	gold quality
cerebellar hemisphere	UBERON:0002245	96.74	gold quality
cerebellar cortex	UBERON:0002129	96.60	gold quality
cortical plate	UBERON:0005343	96.59	gold quality
ganglionic eminence	UBERON:0004023	95.28	gold quality
cerebellum	UBERON:0002037	95.24	gold quality
right frontal lobe	UBERON:0002810	93.74	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	92.40	gold quality
ventricular zone	UBERON:0003053	91.44	gold quality
nucleus accumbens	UBERON:0001882	91.43	gold quality
Brodmann (1909) area 9	UBERON:0013540	91.41	gold quality
spinal cord	UBERON:0002240	90.59	gold quality
anterior cingulate cortex	UBERON:0009835	90.54	gold quality
tibial nerve	UBERON:0001323	90.47	gold quality
putamen	UBERON:0001874	90.32	gold quality
caudate nucleus	UBERON:0001873	90.22	gold quality
left testis	UBERON:0004533	89.96	gold quality
prefrontal cortex	UBERON:0000451	89.71	gold quality
right testis	UBERON:0004534	89.62	gold quality
amygdala	UBERON:0001876	89.53	gold quality
neocortex	UBERON:0001950	88.92	gold quality
frontal cortex	UBERON:0001870	88.80	gold quality
right ovary	UBERON:0002118	88.53	gold quality
hypothalamus	UBERON:0001898	88.48	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	88.42	gold quality
brain	UBERON:0000955	88.35	gold quality
lower esophagus mucosa	UBERON:0035834	87.97	gold quality
testis	UBERON:0000473	87.74	gold quality
forebrain	UBERON:0001890	87.74	gold quality
cerebral cortex	UBERON:0000956	87.47	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	5.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

91 targeting ANKRD13B, 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-29A-3P	100.00	73.11	1835
HSA-MIR-29B-3P	100.00	73.18	1833
HSA-MIR-29C-3P	100.00	73.15	1833
HSA-MIR-3613-3P	100.00	76.36	7965
HSA-MIR-4747-5P	100.00	67.90	2681
HSA-MIR-5196-5P	100.00	67.98	2761
HSA-MIR-6870-5P	99.99	68.55	2115
HSA-MIR-4723-5P	99.97	68.70	2034
HSA-MIR-5698	99.97	68.49	2029
HSA-MIR-7111-5P	99.97	68.48	2062
HSA-MIR-2110	99.96	66.68	1930
HSA-MIR-767-5P	99.95	70.85	993
HSA-MIR-497-5P	99.92	71.83	2674
HSA-MIR-15A-5P	99.90	72.80	2787
HSA-MIR-15B-5P	99.90	72.78	2798
HSA-MIR-16-5P	99.90	72.80	2780
HSA-MIR-195-5P	99.90	72.81	2805
HSA-MIR-627-3P	99.90	71.42	3316
HSA-MIR-5682	99.89	72.56	1005
HSA-MIR-424-5P	99.89	71.90	2641
HSA-MIR-6838-5P	99.89	71.94	2690
HSA-MIR-3151-5P	99.86	63.83	1069
HSA-MIR-8073	99.86	65.21	1118
HSA-MIR-221-5P	99.86	65.45	1052
HSA-MIR-4447	99.85	67.81	2900
HSA-MIR-6756-5P	99.82	67.97	2466
HSA-MIR-4319	99.76	69.83	2586
HSA-MIR-92A-2-5P	99.75	67.01	2164
HSA-MIR-4677-5P	99.70	70.09	1940
HSA-MIR-6766-5P	99.68	67.70	2325

Literature-anchored findings (GeneRIF, showing 1)

• 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)

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	ankrd13b	ENSDARG00000014652
mus_musculus	Ankrd13b	ENSMUSG00000037907
rattus_norvegicus	Ankrd13b	ENSRNOG00000014742
drosophila_melanogaster	CG15118	FBGN0034418
caenorhabditis_elegans		WBGENE00015978

Paralogs (3): ANKRD13A (ENSG00000076513), ANKRD13C (ENSG00000118454), ANKRD13D (ENSG00000172932)

Protein

Protein identifiers

Ankyrin repeat domain-containing protein 13B — Q86YJ7 (reviewed: Q86YJ7)

All UniProt accessions (3): Q86YJ7, K7EKP0, K7ENT0

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 with EGFR (ubiquitinated); the interaction is direct and may regulate EGFR internalization.

Subcellular location. Cell membrane. Late endosome. Early endosome.

Isoforms (2)

UniProt ID	Names	Canonical?
Q86YJ7-1	1	yes
Q86YJ7-2	2

RefSeq proteins (1): NP_689558* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR002110	Ankyrin_rpt	Repeat
IPR003903	UIM_dom	Conserved_site
IPR021832	ANKRD13	Family
IPR036770	Ankyrin_rpt-contain_sf	Homologous_superfamily
IPR055285	ANKRD13_C	Domain

Pfam: PF11904, PF12796

UniProt features (17 total): sequence conflict 4, domain 3, region of interest 3, repeat 2, compositionally biased region 2, chain 1, modified residue 1, splice variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q86YJ7-F1	72.46	0.25

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 (1): 1

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 110 (showing top): TGGTGCT_MIR29A_MIR29B_MIR29C, TGCTGCT_MIR15A_MIR16_MIR15B_MIR195_MIR424_MIR497, AREB6_03, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_DN, GOBP_NEGATIVE_REGULATION_OF_ENDOCYTOSIS, GOBP_VESICLE_MEDIATED_TRANSPORT, GGGTGGRR_PAX4_03, chr17q11, GOBP_REGULATION_OF_VESICLE_MEDIATED_TRANSPORT, GOBP_NEGATIVE_REGULATION_OF_CELLULAR_COMPONENT_ORGANIZATION, GOBP_NEGATIVE_REGULATION_OF_TRANSPORT, MYOD_01, GOBP_REGULATION_OF_RECEPTOR_INTERNALIZATION, GOBP_REGULATION_OF_RECEPTOR_MEDIATED_ENDOCYTOSIS, GOBP_RECEPTOR_INTERNALIZATION

GO Biological Process (1): negative regulation of receptor internalization (GO:0002091)

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

GO Cellular Component (8): cytoplasm (GO:0005737), early endosome (GO:0005769), 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:

Category	Terms
cellular anatomical structure	4
endosome	2
regulation of receptor internalization	1
receptor internalization	1
negative regulation of receptor-mediated endocytosis	1
ubiquitin-like protein reader activity	1
binding	1
intracellular anatomical structure	1
membrane	1
cell periphery	1
cytoplasm	1
endomembrane system	1
cytoplasmic vesicle	1
vacuole	1
plasma membrane	1

Protein interactions and networks

STRING

403 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ANKRD13B	TMEM91	Q6ZNR0	534
ANKRD13B	TMEM25	Q86YD3	533
ANKRD13B	SYNDIG1L	A6NDD5	532
ANKRD13B	DNAJC30	Q96LL9	517
ANKRD13B	PIP5KL1	Q5T9C9	512
ANKRD13B	PRSS48	Q7RTY5	472
ANKRD13B	RTN4RL2	Q86UN3	468
ANKRD13B	EML1	O00423	450
ANKRD13B	SEZ6L2	Q6UXD5	447
ANKRD13B	PLPPR3	Q6T4P5	434
ANKRD13B	ZNF607	Q96SK3	406
ANKRD13B	ZNF568	Q3ZCX4	399
ANKRD13B	CNNM1	Q9NRU3	397
ANKRD13B	ZNF671	Q8TAW3	393
ANKRD13B	PPP6R1	Q9UPN7	388

IntAct

7 interactions, top by confidence:

A	B	Type	Score
GNAI3	RGS12	psi-mi:“MI:0914”(association)	0.640
BOD1L1	MYL6	psi-mi:“MI:0914”(association)	0.350
HDAC1	TRAK1	psi-mi:“MI:0914”(association)	0.350
SLC37A3	PLXNB2	psi-mi:“MI:0914”(association)	0.350
ANKRD13B	RPLP1	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (19): UBC (Reconstituted Complex), ANKRD13B (Affinity Capture-MS), ANKRD13B (Co-fractionation), ANKRD13B (Affinity Capture-MS), ANKRD13B (Affinity Capture-MS), ANKRD13B (Affinity Capture-MS), ANKRD13B (Affinity Capture-MS), VCP (Affinity Capture-MS), VCP (Affinity Capture-Western), ANKRD13B (Affinity Capture-MS), ANKRD13B (Reconstituted Complex), RPLP1 (Two-hybrid), ANKRD13B (Affinity Capture-Western), RNF11 (Affinity Capture-Western), ANKRD13B (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: P42570, Q5F259, Q6KAE5, Q86YJ7, Q99ME3, Q9Y6H5, A4II29, Q28C34, Q3UX43, Q5U5A6, Q6NRD0, Q6PD24, Q6ZTN6, Q7T3Y0, Q7Z6K4, Q7ZUV0, Q7ZYD9, Q80UP5, Q86WC6, Q8IZ07, Q8N6S4, Q91ZA8, Q9D119, Q9TXQ1, A2ZX97, C7B178, P0C550, P19838, P92960, Q0JKV1, Q38849, Q38898, Q38998, Q39128, Q5H9F3, Q5JM04, Q5QNI1, Q652U9, Q653P0, Q6K3T2

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	71
Likely benign	1
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

2160 predictions. Top by Δscore:

Variant	Effect	Δscore
17:29593718:G:GT	donor_gain	1.0000
17:29593734:AG:A	donor_loss	1.0000
17:29593735:GGTAG:G	donor_loss	1.0000
17:29593736:G:GA	donor_loss	1.0000
17:29593737:T:A	donor_loss	1.0000
17:29607739:CA:C	acceptor_loss	1.0000
17:29607740:A:AC	acceptor_loss	1.0000
17:29607740:A:AG	acceptor_gain	1.0000
17:29607740:AGGT:A	acceptor_gain	1.0000
17:29607741:G:GG	acceptor_gain	1.0000
17:29607741:GGTG:G	acceptor_gain	1.0000
17:29607855:G:GT	donor_gain	1.0000
17:29607874:ACAGG:A	donor_loss	1.0000
17:29607875:CAGGT:C	donor_loss	1.0000
17:29607876:AGGTG:A	donor_loss	1.0000
17:29607877:GGT:G	donor_loss	1.0000
17:29607878:GTG:G	donor_loss	1.0000
17:29607984:A:AC	acceptor_loss	1.0000
17:29607984:A:AG	acceptor_gain	1.0000
17:29607984:AGT:A	acceptor_gain	1.0000
17:29607985:G:GC	acceptor_gain	1.0000
17:29607985:GT:G	acceptor_gain	1.0000
17:29607985:GTG:G	acceptor_gain	1.0000
17:29607985:GTGC:G	acceptor_gain	1.0000
17:29607985:GTGCT:G	acceptor_gain	1.0000
17:29607986:T:TA	acceptor_gain	1.0000
17:29608107:CAAG:C	donor_loss	1.0000
17:29608108:AAGG:A	donor_loss	1.0000
17:29608109:AGGT:A	donor_loss	1.0000
17:29608111:GTGA:G	donor_loss	1.0000

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000108303 (17:29614082 AG>A), RS1000390000 (17:29611391 G>A), RS1000467550 (17:29599485 A>G), RS1000622021 (17:29605472 G>A), RS1000743499 (17:29605174 C>A,G), RS1000751389 (17:29596661 C>A,G,T), RS1000758550 (17:29599841 C>T), RS1000841325 (17:29600682 C>T), RS1001177765 (17:29597067 A>G), RS1001379622 (17:29592966 G>A,C), RS1001401119 (17:29606550 T>A,C), RS1001570512 (17:29611468 C>T), RS1001645586 (17:29591897 G>A), RS1001804212 (17:29605847 C>T), RS1001884024 (17:29613658 G>A,C,T)

Disease associations

OMIM: gene MIM:615124 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

6 associations (top):

Study	Trait	p-value
GCST000817_131	Height	7.000000e-09
GCST005194_160	Coronary artery disease	5.000000e-10
GCST005195_69	Coronary artery disease	3.000000e-10
GCST005196_23	Coronary artery disease	6.000000e-10
GCST010703_115	Brain morphology (MOSTest)	1.000000e-28
GCST010866_74	Coronary artery disease	1.000000e-11

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0004346	neuroimaging measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Benzo(a)pyrene	affects methylation, increases expression, increases mutagenesis	4
Valproic Acid	affects expression, decreases expression, increases methylation	3
sodium arsenite	decreases expression, affects cotreatment, increases abundance	2
Cisplatin	affects cotreatment, increases expression, decreases expression	2
Smoke	increases abundance, decreases expression	2
aristolochic acid I	increases expression	1
dicrotophos	increases expression	1
bisphenol A	affects cotreatment, decreases methylation	1
manganese chloride	affects cotreatment, decreases expression, increases abundance	1
CGP 52608	affects binding, increases reaction	1
abrine	decreases expression	1
bisphenol S	increases expression, affects cotreatment	1
jinfukang	affects cotreatment, increases expression	1
(+)-JQ1 compound	decreases expression	1
Sunitinib	increases expression	1
Fulvestrant	affects cotreatment, decreases methylation	1
Air Pollutants	decreases expression, increases abundance	1
Arsenic	affects cotreatment, decreases expression, increases abundance	1
Atrazine	increases expression	1
Dexamethasone	affects cotreatment, increases expression	1
Doxorubicin	decreases expression	1
Estradiol	increases expression	1
Indomethacin	affects cotreatment, increases expression	1
Manganese	increases abundance, affects cotreatment, decreases expression	1
Tobacco Smoke Pollution	decreases expression	1
Tretinoin	decreases expression	1
Triclosan	increases expression	1
1-Methyl-3-isobutylxanthine	affects cotreatment, increases expression	1
Aflatoxin B1	increases expression	1
Acrylamide	decreases expression	1

Clinical trials (associated diseases)

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