ANKRD29

Summary

ANKRD29 (ankyrin repeat domain 29, HGNC:27110) is a protein-coding gene on chromosome 18q11.2, encoding Ankyrin repeat domain-containing protein 29 (Q8N6D5).

Predicted to be located in membrane.

Source: NCBI Gene 147463 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 67 total — 4 pathogenic
• MANE Select transcript: NM_173505

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:27110
Approved symbol	ANKRD29
Name	ankyrin repeat domain 29
Location	18q11.2
Locus type	gene with protein product
Status	Approved
Aliases	FLJ25053
Ensembl gene	ENSG00000154065
Ensembl biotype	protein_coding
Entrez	147463

Gene structure

Transcript identifiers

Ensembl transcripts: 27 — 23 protein_coding, 2 retained_intron, 1 protein_coding_CDS_not_defined, 1 nonsense_mediated_decay

ENST00000322980, ENST00000585908, ENST00000586087, ENST00000586511, ENST00000587763, ENST00000591280, ENST00000591617, ENST00000592179, ENST00000863695, ENST00000863696, ENST00000863697, ENST00000863698, ENST00000863699, ENST00000863700, ENST00000863701, ENST00000863702, ENST00000863703, ENST00000863704, ENST00000863705, ENST00000863706, ENST00000863707, ENST00000965698, ENST00000965699, ENST00000965700, ENST00000965701, ENST00000965702, ENST00000965703

RefSeq mRNA: 2 — MANE Select: NM_173505 NM_001308238, NM_173505

CCDS: CCDS11879, CCDS77164

Canonical transcript exons

ENST00000592179 — 10 exons

Exon	Start	End
ENSE00001109632	23638849	23638947
ENSE00001664111	23646189	23646287
ENSE00001730310	23649083	23649193
ENSE00002295562	23629853	23629951
ENSE00002880487	23662710	23662911
ENSE00002939848	23598926	23601309
ENSE00003528749	23634051	23634149
ENSE00003580052	23612092	23612190
ENSE00003610879	23619531	23619629
ENSE00003635392	23617732	23617827

Expression profiles

Bgee: expression breadth ubiquitous, 229 present calls, max score 93.49.

FANTOM5 (CAGE): breadth broad, TPM avg 1.5430 / max 31.7674, expressed in 577 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter ID	TPM avg	Samples expressed
171365	0.7701	395
171364	0.6304	354
171362	0.1115	54
171363	0.0311	5

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
right lung	UBERON:0002167	93.49	gold quality
parietal pleura	UBERON:0002400	92.23	gold quality
upper lobe of left lung	UBERON:0008952	91.59	gold quality
upper lobe of lung	UBERON:0008948	91.08	gold quality
right uterine tube	UBERON:0001302	90.65	gold quality
lung	UBERON:0002048	89.67	gold quality
body of uterus	UBERON:0009853	89.52	gold quality
visceral pleura	UBERON:0002401	88.84	gold quality
left uterine tube	UBERON:0001303	88.65	gold quality
subcutaneous adipose tissue	UBERON:0002190	88.28	gold quality
omental fat pad	UBERON:0010414	87.99	gold quality
peritoneum	UBERON:0002358	87.95	gold quality
adipose tissue of abdominal region	UBERON:0007808	87.63	gold quality
lymph node	UBERON:0000029	87.43	gold quality
endothelial cell	CL:0000115	87.14	gold quality
smooth muscle tissue	UBERON:0001135	87.07	gold quality
germinal epithelium of ovary	UBERON:0001304	86.80	gold quality
ectocervix	UBERON:0012249	86.08	gold quality
primary visual cortex	UBERON:0002436	85.75	gold quality
adipose tissue	UBERON:0001013	85.74	gold quality
left ovary	UBERON:0002119	85.55	gold quality
lower lobe of lung	UBERON:0008949	85.19	gold quality
right ovary	UBERON:0002118	85.13	gold quality
apex of heart	UBERON:0002098	85.04	gold quality
cauda epididymis	UBERON:0004360	84.91	gold quality
superficial temporal artery	UBERON:0001614	84.47	gold quality
right coronary artery	UBERON:0001625	84.43	gold quality
vagina	UBERON:0000996	84.38	gold quality
calcaneal tendon	UBERON:0003701	84.32	gold quality
endocervix	UBERON:0000458	84.00	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	8.78

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

139 targeting ANKRD29, 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-9-5P	100.00	72.28	2361
HSA-MIR-4795-3P	100.00	74.62	4024
HSA-MIR-4776-3P	100.00	68.73	1340
HSA-MIR-126-5P	100.00	72.71	3180
HSA-MIR-33A-5P	99.99	68.62	1055
HSA-MIR-33B-5P	99.99	68.58	1062
HSA-MIR-186-5P	99.99	70.83	3707
HSA-MIR-19A-3P	99.98	75.33	2762
HSA-MIR-19B-3P	99.98	75.44	2754
HSA-MIR-5696	99.98	72.36	4487
HSA-MIR-302C-5P	99.97	72.56	3642
HSA-MIR-302E	99.96	70.74	2669
HSA-MIR-590-3P	99.96	74.34	6478
HSA-LET-7C-3P	99.95	73.42	2862
HSA-MIR-1-3P	99.93	72.35	1914
HSA-MIR-206	99.93	72.50	1893
HSA-MIR-335-3P	99.93	73.36	4958
HSA-MIR-3119	99.92	71.34	2390
HSA-MIR-613	99.91	71.50	1710
HSA-MIR-8063	99.91	69.76	3146
HSA-MIR-106A-5P	99.90	73.94	2683
HSA-MIR-627-3P	99.90	71.42	3316
HSA-MIR-17-5P	99.89	73.83	2665
HSA-MIR-302A-3P	99.89	71.23	1777
HSA-MIR-302B-3P	99.89	71.23	1777
HSA-MIR-302C-3P	99.89	71.20	1778
HSA-MIR-302D-3P	99.89	71.25	1777
HSA-MIR-106B-5P	99.88	74.72	2795
HSA-MIR-20A-5P	99.88	74.76	2769
HSA-MIR-20B-5P	99.88	74.01	2621

Literature-anchored findings (GeneRIF, showing 1)

• ANKRD29, as a new prognostic and immunological biomarker of non-small cell lung cancer, inhibits cell growth and migration by regulating MAPK signaling pathway. (PMID:37277814)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	ankrd29	ENSDARG00000057159
mus_musculus	Ankrd29	ENSMUSG00000057766
rattus_norvegicus	Ankrd29	ENSRNOG00000046744

Paralogs (1): ASB12 (ENSG00000198881)

Protein

Protein identifiers

Ankyrin repeat domain-containing protein 29 — Q8N6D5 (reviewed: Q8N6D5)

All UniProt accessions (4): Q8N6D5, K7EL63, K7EQM1, V9GYT2

UniProt curated annotations — full annotation on UniProt →

Isoforms (2)

UniProt ID	Names	Canonical?
Q8N6D5-1	1	yes
Q8N6D5-3	3

RefSeq proteins (2): NP_001295167, NP_775776* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR002110	Ankyrin_rpt	Repeat
IPR036770	Ankyrin_rpt-contain_sf	Homologous_superfamily
IPR050889	Dendritic_Spine_Reg/Scaffold	Family

Pfam: PF00023, PF12796

UniProt features (12 total): repeat 8, sequence variant 2, chain 1, splice variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8N6D5-F1	91.86	0.84

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 99 (showing top): TGCACTT_MIR519C_MIR519B_MIR519A, GAUSSMANN_MLL_AF4_FUSION_TARGETS_A_UP, PICCALUGA_ANGIOIMMUNOBLASTIC_LYMPHOMA_UP, CAATGCA_MIR33, ACATTCC_MIR1_MIR206, DODD_NASOPHARYNGEAL_CARCINOMA_UP, BASAKI_YBX1_TARGETS_DN, DOUGLAS_BMI1_TARGETS_UP, CUI_TCF21_TARGETS_2_DN, chr18q11, ACEVEDO_LIVER_CANCER_WITH_H3K27ME3_DN, TGATTTRY_GFI1_01, SENGUPTA_NASOPHARYNGEAL_CARCINOMA_UP, CSR_LATE_UP.V1_DN, TRAYNOR_RETT_SYNDROM_UP

GO Biological Process (0):

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

GO Cellular Component (1): membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
binding	1
cellular anatomical structure	1

Protein interactions and networks

STRING

1214 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ANKRD29	SPACA9	Q96E40	541
ANKRD29	SLC35D4	Q24JQ0	527
ANKRD29	SERPINE3	A8MV23	500
ANKRD29	ADGRL4	Q9HBW9	455
ANKRD29	FAM124A	Q86V42	447
ANKRD29	OLFML2A	Q68BL7	447
ANKRD29	SPSB3	Q6PJ21	444
ANKRD29	LAMA3	Q16787	419
ANKRD29	ARAP2	Q8WZ64	401
ANKRD29	MROH9	Q5TGP6	401
ANKRD29	CDH22	Q9UJ99	398
ANKRD29	KLHL38	Q2WGJ6	393
ANKRD29	GREB1L	Q9C091	392
ANKRD29	SYNGR4	O95473	376
ANKRD29	LAMA4	Q16363	372

IntAct

36 interactions, top by confidence:

A	B	Type	Score
FAM90A1	ANKRD29	psi-mi:“MI:0915”(physical association)	0.560
GTF2H5	ANKRD29	psi-mi:“MI:0915”(physical association)	0.560
ANKRD29	CABP2	psi-mi:“MI:0915”(physical association)	0.560
FERMT3	ANKRD29	psi-mi:“MI:0915”(physical association)	0.560
HLCS	ANKRD29	psi-mi:“MI:0915”(physical association)	0.560
ANKRD29	MRPL53	psi-mi:“MI:0915”(physical association)	0.560
ANKRD29	USP32	psi-mi:“MI:0915”(physical association)	0.560
ANKRD29	RABGEF1	psi-mi:“MI:0915”(physical association)	0.560
GYPA	ANKRD29	psi-mi:“MI:0915”(physical association)	0.560
ANKRD29	CRACR2A	psi-mi:“MI:0915”(physical association)	0.560
ANKRD29	ADD1	psi-mi:“MI:0914”(association)	0.530
ANKRD29	ADD1	psi-mi:“MI:0914”(association)	0.350
M		psi-mi:“MI:0914”(association)	0.350
ANKRD29	PIPSL	psi-mi:“MI:0914”(association)	0.350
ANKRD29	HMOX2	psi-mi:“MI:0914”(association)	0.350
GTF2H5	ANKRD29	psi-mi:“MI:0915”(physical association)	0.000
CABP2	ANKRD29	psi-mi:“MI:0915”(physical association)	0.000
RABGEF1	ANKRD29	psi-mi:“MI:0915”(physical association)	0.000
GYPA	ANKRD29	psi-mi:“MI:0915”(physical association)	0.000
CRACR2A	ANKRD29	psi-mi:“MI:0915”(physical association)	0.000
FERMT3	ANKRD29	psi-mi:“MI:0915”(physical association)	0.000
HLCS	ANKRD29	psi-mi:“MI:0915”(physical association)	0.000
MRPL53	ANKRD29	psi-mi:“MI:0915”(physical association)	0.000
USP32	ANKRD29	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (30): YTHDF1 (Affinity Capture-MS), ADD2 (Affinity Capture-MS), ADD1 (Affinity Capture-MS), FAM122B (Affinity Capture-MS), UBP1 (Affinity Capture-MS), TFCP2 (Affinity Capture-MS), ADD3 (Affinity Capture-MS), ADD3 (Affinity Capture-MS), ADD2 (Affinity Capture-MS), FAM122B (Affinity Capture-MS), UBP1 (Affinity Capture-MS), ADD1 (Affinity Capture-MS), TFCP2 (Affinity Capture-MS), ANKRD29 (Two-hybrid), ANKRD29 (Two-hybrid)

ESM2 similar proteins: A0A2R8QFQ6, A0A2R8RWN9, A6H779, B5DFK7, O35345, O60684, Q01730, Q15303, Q15404, Q17QS6, Q28D01, Q2HJ19, Q3ULA2, Q502M6, Q503E9, Q58DG6, Q5E9C0, Q5R3Z8, Q5R4Q7, Q5RBV0, Q5SP67, Q5SRY7, Q5XIJ5, Q5ZIN0, Q5ZJX1, Q61527, Q62956, Q67FW5, Q6DD70, Q6GL10, Q862Z2, Q8BH16, Q8C6G8, Q8N653, Q8N6D5, Q8VBX0, Q8VCV1, Q8VEG6, Q8WXK3, Q91854

Diamond homologs: B0G124, B4E2M5, C7B178, L7XCU0, O43150, O75762, O95271, P25631, P28492, P77736, Q01317, Q0VC93, Q10728, Q28FJ2, Q3KP44, Q3SX45, Q3UES3, Q3UMT1, Q3UX43, Q3V096, Q4R7L8, Q569N2, Q571F8, Q5EA33, Q5RD76, Q5SUE8, Q5U464, Q5ZLC6, Q5ZLC8, Q6AI12, Q6PFX9, Q6RI86, Q7SIG6, Q7XUW4, Q7Z713, Q86WC6, Q8BTI7, Q8N6D5, Q8N9B4, Q8NB46

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	4
Likely pathogenic	0
Uncertain significance	58
Likely benign	2
Benign	0

Top pathogenic / likely-pathogenic (4)

Variant ID	HGVS	Classification
144654	GRCh38/hg38 18p11.32-q23(chr18:149089-80234391)x3	Pathogenic
3242762	NC_000018.9:g.(?20516815)(21534612_?)del	Pathogenic
3384215	Single allele	Pathogenic
443062	GRCh37/hg19 18q11.2-12.2(chr18:20069932-36887326)x1	Pathogenic

SpliceAI

2013 predictions. Top by Δscore:

Variant	Effect	Δscore
18:23601305:TTGGC:T	acceptor_gain	1.0000
18:23601307:GGCC:G	acceptor_loss	1.0000
18:23601308:GCCT:G	acceptor_loss	1.0000
18:23601310:C:CC	acceptor_gain	1.0000
18:23601310:CTGAA:C	acceptor_loss	1.0000
18:23618643:G:C	donor_gain	1.0000
18:23629950:TC:T	acceptor_gain	1.0000
18:23629951:CC:C	acceptor_gain	1.0000
18:23634049:A:AC	donor_gain	1.0000
18:23634050:C:CC	donor_gain	1.0000
18:23638847:A:AC	donor_gain	1.0000
18:23638848:C:CC	donor_gain	1.0000
18:23649011:ATT:A	donor_gain	1.0000
18:23649013:T:A	donor_gain	1.0000
18:23649081:A:AC	donor_gain	1.0000
18:23649082:C:CC	donor_gain	1.0000
18:23649082:CG:C	donor_gain	1.0000
18:23662705:CTCA:C	donor_loss	1.0000
18:23662706:TCACC:T	donor_loss	1.0000
18:23662707:CAC:C	donor_loss	1.0000
18:23662708:A:AC	donor_gain	1.0000
18:23662708:AC:A	donor_gain	1.0000
18:23662709:C:CC	donor_gain	1.0000
18:23662709:CC:C	donor_gain	1.0000
18:23601306:TGGC:T	acceptor_gain	0.9900
18:23601307:GGC:G	acceptor_gain	0.9900
18:23601308:GC:G	acceptor_gain	0.9900
18:23601309:CC:C	acceptor_gain	0.9900
18:23619529:A:AC	donor_gain	0.9900
18:23619530:C:CC	donor_gain	0.9900

AlphaMissense

1939 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
18:23617800:C:G	A219P	0.996
18:23634124:G:T	A119D	0.996
18:23629924:C:G	A153P	0.995
18:23634120:A:C	S120R	0.995
18:23634120:A:T	S120R	0.995
18:23634122:T:G	S120R	0.995
18:23638920:C:G	A87P	0.995
18:23619604:G:T	A185E	0.994
18:23638919:G:T	A87D	0.994
18:23638922:G:T	A86D	0.994
18:23612166:C:G	A250P	0.993
18:23629926:G:T	A152D	0.993
18:23634125:C:G	A119P	0.993
18:23617803:C:G	A218P	0.992
18:23619565:A:G	L198P	0.992
18:23619611:A:G	W183R	0.992
18:23619611:A:T	W183R	0.992
18:23629923:G:T	A153D	0.992
18:23646226:A:G	L65P	0.992
18:23617799:G:T	A219D	0.991
18:23634085:A:G	L132P	0.991
18:23612129:A:G	L262P	0.989
18:23646262:G:T	A53D	0.989
18:23629890:A:G	L164P	0.988
18:23629927:C:G	A152P	0.988
18:23638886:A:G	L98P	0.988
18:23638923:C:G	A86P	0.988
18:23646260:C:G	A54P	0.988
18:23612165:G:T	A250E	0.987
18:23619602:A:G	S186P	0.987

dbSNP variants (sampled 300 via entrez): RS1000011610 (18:23615897 A>T), RS1000021902 (18:23607501 A>G), RS1000057829 (18:23609235 T>C), RS1000104608 (18:23648556 C>G,T), RS1000116198 (18:23609834 C>T), RS1000182427 (18:23652123 C>T), RS1000258783 (18:23645438 G>A), RS1000316685 (18:23627850 A>C,G), RS1000365447 (18:23645927 T>C), RS1000367494 (18:23620466 G>A), RS1000396806 (18:23602814 T>A), RS1000442895 (18:23615546 C>A), RS1000530821 (18:23640153 G>A), RS1000548756 (18:23647213 T>C), RS1000639224 (18:23651861 T>C,G)

Disease associations

OMIM: gene `` | disease phenotypes: MIM:257220, MIM:601808

GenCC curated gene-disease

Mondo (2): Niemann-Pick disease, type C1 (MONDO:0009757), chromosome 18q deletion syndrome (MONDO:0011147)

Orphanet (3): Niemann-Pick disease type C (Orphanet:646), Monosomy 18q syndrome (Orphanet:1600), Partial deletion of the long arm of chromosome 18 syndrome (Orphanet:262146)

HPO phenotypes

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

GWAS associations

1 associations (top):

Study	Trait	p-value
GCST002283_4	Amyotrophic lateral sclerosis (sporadic)	8.000000e-06

MeSH disease descriptors (1)

Descriptor	Name	Tree numbers
C536580	Chromosome 18 deletion syndrome (supp.)

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.

Chemical	Actions (top 5)	PubMed papers
Estradiol	affects cotreatment, decreases expression, increases expression	3
Nickel	decreases expression	2
aristolochic acid I	increases expression	1
propionaldehyde	increases expression	1
bisphenol A	decreases methylation	1
terbufos	increases methylation	1
trichostatin A	increases expression	1
tris(1,3-dichloro-2-propyl)phosphate	increases expression	1
polyhexamethyleneguanidine	affects expression	1
CGP 52608	increases reaction, affects binding	1
ICG 001	increases expression	1
abrine	decreases expression	1
jinfukang	affects cotreatment, increases expression	1
(+)-JQ1 compound	decreases expression	1
Temozolomide	decreases expression	1
Sunitinib	increases expression	1
Arsenic Trioxide	decreases expression	1
Acetaminophen	decreases expression	1
Arsenic	affects methylation	1
Cisplatin	affects cotreatment, increases expression	1
Fonofos	increases methylation	1
Formaldehyde	increases expression	1
Methyl Methanesulfonate	decreases expression	1
Parathion	increases methylation	1
Silicon Dioxide	increases expression	1
Tobacco Smoke Pollution	affects expression	1
Valproic Acid	increases expression	1
7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide	increases expression	1
Cyclosporine	decreases expression	1
Antirheumatic Agents	increases expression	1

Clinical trials (associated diseases)

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

Trial	Phase	Status	Title
NCT04860960	PHASE3	ACTIVE_NOT_RECRUITING	Phase 3 Study to Evaluate Intravenous Trappsol(R) Cyclo(TM) in Pediatric and Adult Patients With Niemann-Pick Disease Type C1
NCT01747135	PHASE1	COMPLETED	Hydroxypropyl Beta Cyclodextrin for Niemann-Pick Type C1 Disease
NCT02939547	PHASE1	COMPLETED	Study of the Pharmacokinetics of Trappsol and Effects on Potential Biomarkers of Niemann-Pick C1 (NPC1)
NCT03893071	PHASE1	UNKNOWN	Open-Label Study of Long-Term Safety and Efficacy of Intravenous Trappsol Cyclo (HPβCD) in Niemann-Pick Disease Type C
NCT02912793	PHASE1/PHASE2	COMPLETED	Safety and Efficacy of Intravenous Trappsol Cyclo (HPBCD) in Niemann-Pick Type C Patients
NCT03887533	PHASE1/PHASE2	TERMINATED	Combined Intrathecal and Intravenous VTS-270 Therapy for Liver and Neurological Disease Associated With Niemann-Pick Disease, Type C1
NCT03201627	EARLY_PHASE1	UNKNOWN	Study of Lithium Carbonate to Treat Niemann-Pick Type C1 Disease
NCT03655223	Not specified	ENROLLING_BY_INVITATION	Early Check: Expanded Screening in Newborns
NCT05642221	Not specified	COMPLETED	Functional Near-Infrared Spectroscopy (fNIRS) Combined With Diffuse Correlation Spectroscopy (DCS) in Neurocognitive Disease as Compared to Healthy Neurotypical Controls