ANKRD40

Summary

ANKRD40 (ankyrin repeat domain 40, HGNC:28233) is a protein-coding gene on chromosome 17q21.33, encoding Ankyrin repeat domain-containing protein 40 (Q6AI12).

At a glance

• Clinical variants (ClinVar): 41 total
• MANE Select transcript: NM_052855

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:28233
Approved symbol	ANKRD40
Name	ankyrin repeat domain 40
Location	17q21.33
Locus type	gene with protein product
Status	Approved
Aliases	MGC15396
Ensembl gene	ENSG00000154945
Ensembl biotype	protein_coding
Entrez	91369

Gene structure

Transcript identifiers

Ensembl transcripts: 4 — 3 protein_coding, 1 retained_intron

ENST00000285243, ENST00000507114, ENST00000513072, ENST00000943233

RefSeq mRNA: 1 — MANE Select: NM_052855 NM_052855

CCDS: CCDS11572

Canonical transcript exons

ENST00000285243 — 5 exons

Exon	Start	End
ENSE00001018550	50696940	50697121
ENSE00001018552	50700568	50700716
ENSE00001018556	50699399	50699893
ENSE00001109908	50707521	50707914
ENSE00001331498	50693198	50696143

Expression profiles

Bgee: expression breadth ubiquitous, 277 present calls, max score 99.20.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 21.8595 / max 339.5356, expressed in 1805 samples.

FANTOM5 promoters (5 alternative TSS)

Promoter ID	TPM avg	Samples expressed
166992	11.7504	1781
166989	5.4887	1711
166991	3.8154	1493
166990	0.5996	314
166993	0.2054	79

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
medial globus pallidus	UBERON:0002477	99.20	gold quality
globus pallidus	UBERON:0001875	99.04	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	98.56	gold quality
lateral globus pallidus	UBERON:0002476	98.16	gold quality
substantia nigra pars reticulata	UBERON:0001966	98.12	gold quality
subthalamic nucleus	UBERON:0001906	97.94	gold quality
inferior vagus X ganglion	UBERON:0005363	97.87	gold quality
spinal cord	UBERON:0002240	97.56	gold quality
substantia nigra pars compacta	UBERON:0001965	97.51	gold quality
superior vestibular nucleus	UBERON:0007227	96.57	gold quality
lateral nuclear group of thalamus	UBERON:0002736	96.43	gold quality
corpus callosum	UBERON:0002336	96.21	gold quality
pons	UBERON:0000988	96.00	gold quality
amygdala	UBERON:0001876	95.92	gold quality
ventral tegmental area	UBERON:0002691	95.71	gold quality
gastrocnemius	UBERON:0001388	95.63	gold quality
muscle of leg	UBERON:0001383	95.37	gold quality
hindlimb stylopod muscle	UBERON:0004252	95.04	gold quality
putamen	UBERON:0001874	94.73	gold quality
skeletal muscle tissue of rectus abdominis	UBERON:0004511	94.70	gold quality
caudate nucleus	UBERON:0001873	94.54	gold quality
Ammon’s horn	UBERON:0001954	94.34	gold quality
nucleus accumbens	UBERON:0001882	94.29	gold quality
temporal lobe	UBERON:0001871	93.97	gold quality
colonic epithelium	UBERON:0000397	93.39	gold quality
biceps brachii	UBERON:0001507	93.21	gold quality
trigeminal ganglion	UBERON:0001675	92.98	gold quality
dorsal plus ventral thalamus	UBERON:0001897	92.94	gold quality
midbrain	UBERON:0001891	92.83	gold quality
skeletal muscle tissue of biceps brachii	UBERON:0004502	92.56	gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-ANND-3	yes	10.65
E-GEOD-106540	no	117.68

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

193 targeting ANKRD40, 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-429	100.00	73.44	2698
HSA-MIR-200B-3P	100.00	73.31	2693
HSA-MIR-200C-3P	100.00	73.35	2685
HSA-MIR-340-5P	100.00	72.50	4437
HSA-MIR-3163	100.00	77.23	8605
HSA-MIR-3613-3P	100.00	76.36	7965
HSA-MIR-8485	100.00	77.57	4731
HSA-MIR-188-3P	100.00	68.76	1240
HSA-MIR-7110-3P	100.00	73.18	2486
HSA-MIR-6833-3P	100.00	70.63	3197
HSA-MIR-4768-5P	100.00	69.49	2861
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-223-3P	99.99	70.14	1140
HSA-MIR-371B-5P	99.99	75.34	4759
HSA-MIR-6077	99.99	68.04	2299
HSA-MIR-499A-5P	99.98	70.79	1323
HSA-MIR-4775	99.98	75.00	6394
HSA-MIR-9985	99.98	72.11	2939
HSA-MIR-373-5P	99.98	75.36	4753
HSA-MIR-616-5P	99.98	75.58	4775
HSA-MIR-27A-3P	99.98	72.13	2955
HSA-MIR-27B-3P	99.98	72.13	2955
HSA-MIR-520D-5P	99.98	73.34	4883
HSA-MIR-524-5P	99.98	73.43	4882
HSA-MIR-3148	99.97	75.06	6478
HSA-MIR-3065-5P	99.97	71.56	3281
HSA-MIR-590-3P	99.96	74.34	6478
HSA-MIR-5688	99.96	73.23	4504
HSA-MIR-495-3P	99.96	72.81	4197
HSA-MIR-128-3P	99.95	71.17	2484

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	ankrd40	ENSDARG00000076490
mus_musculus	Ankrd40	ENSMUSG00000020864
rattus_norvegicus	Ankrd40	ENSRNOG00000002935
rattus_norvegicus	Ankrd40	ENSRNOG00000063936

Paralogs (1): ANKRD40CL (ENSG00000167117)

Protein

Protein identifiers

Ankyrin repeat domain-containing protein 40 — Q6AI12 (reviewed: Q6AI12)

All UniProt accessions (3): Q6AI12, A8IK34, K7ERW4

RefSeq proteins (1): NP_443087* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR002110	Ankyrin_rpt	Repeat
IPR036770	Ankyrin_rpt-contain_sf	Homologous_superfamily
IPR039195	ANKRD40	Family

Pfam: PF13637

UniProt features (11 total): region of interest 3, compositionally biased region 3, repeat 2, chain 1, sequence conflict 1, modified residue 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q6AI12-F1	69.38	0.39

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: 175 (showing top): TONKS_TARGETS_OF_RUNX1_RUNX1T1_FUSION_MONOCYTE_UP, AAGCCAT_MIR135A_MIR135B, BROWNE_HCMV_INFECTION_16HR_UP, TGANTCA_AP1_C, ABBUD_LIF_SIGNALING_1_DN, GFI1_01, GCM_NF2, CREBP1_01, NIKOLSKY_BREAST_CANCER_17Q21_Q25_AMPLICON, AP2_Q6_01, YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_7, TEF_Q6, RB_DN.V1_DN, PDGF_ERK_DN.V1_DN, STK33_UP

GO Biological Process (1): biological_process (GO:0008150)

GO Molecular Function (2): molecular_function (GO:0003674), protein binding (GO:0005515)

GO Cellular Component (1): cellular_component (GO:0005575)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
binding	1

Protein interactions and networks

STRING

774 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ANKRD40	SUPT20H	Q8NEM7	586
ANKRD40	LHFPL1	Q86WI0	446
ANKRD40	FAM204A	Q9H8W3	435
ANKRD40	PPP1R12C	Q9BZL4	419
ANKRD40	TPGS2	Q68CL5	408
ANKRD40	DDX17	Q92841	404
ANKRD40	C7orf25	Q9BPX7	400
ANKRD40	MIX23	Q4VC31	390
ANKRD40	ANKMY2	Q8IV38	389
ANKRD40	THAP5	Q7Z6K1	375
ANKRD40	SESTD1	Q86VW0	374
ANKRD40	THSD7B	Q9C0I4	364
ANKRD40	COPG2	Q9UBF2	354
ANKRD40	ABTB2	Q8N961	352
ANKRD40	TMEM109	Q9BVC6	340
ANKRD40	AGGF1	Q8N302	340

IntAct

128 interactions, top by confidence:

A	B	Type	Score
ANKRD40	AHCY	psi-mi:“MI:0915”(physical association)	0.900
AHCY	ANKRD40	psi-mi:“MI:0915”(physical association)	0.900
ANKRD40	AHCY	psi-mi:“MI:0914”(association)	0.900
ANKRD40	PIN1	psi-mi:“MI:0915”(physical association)	0.720
PIN1	ANKRD40	psi-mi:“MI:0915”(physical association)	0.720
LTA	ANKRD40	psi-mi:“MI:0915”(physical association)	0.640
FBXW7	MYCBP2	psi-mi:“MI:0914”(association)	0.640
ULK4	ANKRD40	psi-mi:“MI:0915”(physical association)	0.590
ANKRD40	SDCBP	psi-mi:“MI:0915”(physical association)	0.560
ANKRD40	RAD23A	psi-mi:“MI:0915”(physical association)	0.560
SDCBP	ANKRD40	psi-mi:“MI:0915”(physical association)	0.560
RCBTB1	ANKRD40	psi-mi:“MI:0915”(physical association)	0.560
RFC3	ANKRD40	psi-mi:“MI:0915”(physical association)	0.560
RCBTB1	ANKRD40	psi-mi:“MI:0914”(association)	0.560
C1orf94	USO1	psi-mi:“MI:0914”(association)	0.550
SOX5	SOX1	psi-mi:“MI:0914”(association)	0.530
PIGT	ZNF609	psi-mi:“MI:0914”(association)	0.530
AHCY	AHCYL1	psi-mi:“MI:0914”(association)	0.530

BioGRID (117): ANKRD40 (Two-hybrid), ANKRD40 (Two-hybrid), ANKRD40 (Two-hybrid), ANKRD40 (Two-hybrid), ANKRD40 (Two-hybrid), ANKRD40 (Affinity Capture-RNA), ANKRD40 (Affinity Capture-RNA), ANKRD40 (Affinity Capture-MS), ANKRD40 (Affinity Capture-MS), ANKRD40 (Affinity Capture-MS), ANKRD40 (Affinity Capture-MS), ANKRD40 (Affinity Capture-MS), ANKRD40 (Affinity Capture-MS), ANKRD40 (Affinity Capture-MS), ANKRD40 (Two-hybrid)

ESM2 similar proteins: A0FIN4, A2VD01, A9ZLX4, D2HNW6, D4A7U2, O88974, O94988, P10914, P14316, P15314, P16236, P17433, P17947, P23570, P23906, P49140, Q00IB7, Q13506, Q13905, Q15047, Q1LY51, Q3B7M3, Q3SZP0, Q3TTA7, Q3UWM4, Q4V7W5, Q5HYC2, Q5RJA1, Q5XJV7, Q61122, Q62722, Q6A098, Q6AI12, Q6BDS1, Q6DFR2, Q6GQL0, Q6PKU1, Q6ZMT4, Q6ZNC4, Q80TJ7

Diamond homologs: A4II29, E9Q238, F1MJR8, O83515, P0C0T2, Q01317, Q05823, Q05921, Q14678, Q1LZH7, Q21920, Q24009, Q5M9H0, Q5SUE8, Q5U4T7, Q5U5A6, Q5XJ13, Q68DC2, Q6AI12, Q6GQX6, Q6NY19, Q6ZW76, Q7T3X9, Q7T3Y0, Q7Z6K4, Q8BX02, Q8IWB6, Q91ZA8, Q99MQ1, Q9CZK6, Q9H694, Q9IA00, Q9Z1P7, A0A072VIM5, A0A0K0PU92, A2CIR7, G3LSH3, G5EGA3, G8GTN7, Q2HW56

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	38
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

687 predictions. Top by Δscore:

Variant	Effect	Δscore
17:50696934:TCTTA:T	donor_loss	1.0000
17:50696935:CTTA:C	donor_loss	1.0000
17:50696936:TTAC:T	donor_loss	1.0000
17:50696937:TACC:T	donor_loss	1.0000
17:50696938:ACC:A	donor_loss	1.0000
17:50696938:ACCTT:A	donor_gain	1.0000
17:50696939:C:CG	donor_loss	1.0000
17:50696939:CCTT:C	donor_gain	1.0000
17:50696939:CCTTC:C	donor_gain	1.0000
17:50696942:T:A	donor_gain	1.0000
17:50697117:CAGCT:C	acceptor_gain	1.0000
17:50697118:AGCT:A	acceptor_gain	1.0000
17:50697118:AGCTC:A	acceptor_gain	1.0000
17:50697119:GCTCT:G	acceptor_gain	1.0000
17:50697120:CT:C	acceptor_gain	1.0000
17:50697122:C:CC	acceptor_gain	1.0000
17:50697123:T:A	acceptor_loss	1.0000
17:50699891:CCA:C	acceptor_gain	1.0000
17:50699891:CCACT:C	acceptor_gain	1.0000
17:50699892:CAC:C	acceptor_gain	1.0000
17:50699894:C:CC	acceptor_gain	1.0000
17:50699895:T:C	acceptor_gain	1.0000
17:50699895:T:TC	acceptor_gain	1.0000
17:50700580:T:TA	donor_gain	1.0000
17:50696938:A:AC	donor_gain	0.9900
17:50696939:C:CC	donor_gain	0.9900
17:50697120:CTCT:C	acceptor_gain	0.9900
17:50699363:C:A	donor_gain	0.9900
17:50699834:ACT:A	donor_gain	0.9900
17:50699835:CTC:C	donor_gain	0.9900

AlphaMissense

2386 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
17:50700663:A:G	L63P	1.000
17:50700701:C:A	W50C	1.000
17:50700701:C:G	W50C	1.000
17:50700703:A:G	W50R	1.000
17:50700703:A:T	W50R	1.000
17:50696106:A:G	L333P	0.999
17:50696124:A:G	L327P	0.999
17:50696133:A:T	V324D	0.999
17:50696959:G:T	P314H	0.999
17:50696960:G:A	P314S	0.999
17:50696966:T:C	K312E	0.999
17:50696967:T:A	R311S	0.999
17:50696967:T:G	R311S	0.999
17:50697069:G:C	F277L	0.999
17:50697069:G:T	F277L	0.999
17:50697071:A:G	F277L	0.999
17:50697108:C:A	K264N	0.999
17:50697108:C:G	K264N	0.999
17:50697112:A:G	L263P	0.999
17:50700663:A:T	L63Q	0.999
17:50700710:A:C	C47W	0.999
17:50707602:G:T	A18E	0.999
17:50707606:C:G	A17P	0.999
17:50707614:A:G	L14P	0.999
17:50696114:G:C	F330L	0.998
17:50696114:G:T	F330L	0.998
17:50696116:A:G	F330L	0.998
17:50696124:A:T	L327H	0.998
17:50696962:A:G	L313S	0.998
17:50696964:C:A	K312N	0.998

dbSNP variants (sampled 300 via entrez): RS1000104132 (17:50704655 T>A), RS1000171499 (17:50706018 A>G), RS1000357228 (17:50707146 C>G), RS1000389796 (17:50707341 G>A,C), RS1000533222 (17:50704381 T>C), RS1000927836 (17:50697231 C>A), RS1000960394 (17:50696725 C>T), RS1001025262 (17:50700297 G>C), RS1001706887 (17:50694219 C>T), RS1001935172 (17:50706104 A>C), RS1002092660 (17:50699723 G>C), RS1002172490 (17:50703689 C>A,T), RS1002362476 (17:50695764 C>A,T), RS1002413078 (17:50696352 C>T), RS1002640092 (17:50702329 G>T)

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

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

20 total (human), top 20 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Cadmium Chloride	decreases expression, increases abundance	2
triphenyl phosphate	affects expression	1
bisphenol A	increases expression	1
sodium arsenite	decreases expression	1
perfluorooctanoic acid	decreases expression	1
benzo(e)pyrene	increases methylation	1
4-aminophenylarsenoxide	affects binding, decreases reaction	1
CGP 52608	affects binding, increases reaction	1
perfluoro-n-nonanoic acid	decreases expression	1
perfluorohexanesulfonic acid	decreases expression	1
4-(4-((5-(4,5-dimethyl-2-nitrophenyl)-2-furanyl)methylene)-4,5-dihydro-3-methyl-5-oxo-1H-pyrazol-1-yl)benzoic acid	decreases expression	1
Sunitinib	increases expression	1
Arsenic Trioxide	affects binding, decreases reaction	1
Atrazine	increases expression	1
Cadmium	increases abundance, decreases expression	1
Doxorubicin	decreases expression	1
Hydrogen Peroxide	increases expression	1
Methapyrilene	increases methylation	1
Thiram	decreases expression	1
Tretinoin	decreases expression	1

Cellosaurus cell lines

1 cell lines: 1 cancer cell line

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

Cellosaurus	Name	Category	Sex
CVCL_E1QF	HAP1 ANKRD40 (-)	Cancer cell line	Male

Clinical trials (associated diseases)

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