ARMH3

Summary

ARMH3 (armadillo like helical domain containing 3, HGNC:25788) is a protein-coding gene on chromosome 10q24.32, encoding Armadillo-like helical domain-containing protein 3 (Q5T2E6). Involved in GBF1 recruitment, Golgi maintenance and protein secretion.

Involved in regulation of Golgi organization. Located in Golgi membrane and cytosol.

Source: NCBI Gene 79591 — RefSeq curated summary.

At a glance

• GWAS associations: 12
• Clinical variants (ClinVar): 20 total
• MANE Select transcript: NM_024541

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:25788
Approved symbol	ARMH3
Name	armadillo like helical domain containing 3
Location	10q24.32
Locus type	gene with protein product
Status	Approved
Aliases	FLJ13114, DGARM
Ensembl gene	ENSG00000120029
Ensembl biotype	protein_coding
OMIM	620867
Entrez	79591

Gene structure

Transcript identifiers

Ensembl transcripts: 34 — 32 protein_coding, 2 protein_coding_CDS_not_defined

ENST00000311122, ENST00000370033, ENST00000456149, ENST00000470043, ENST00000495001, ENST00000896854, ENST00000896855, ENST00000896856, ENST00000896857, ENST00000896858, ENST00000896859, ENST00000896860, ENST00000896861, ENST00000896862, ENST00000896863, ENST00000921907, ENST00000921908, ENST00000921909, ENST00000921910, ENST00000921911, ENST00000921912, ENST00000921913, ENST00000951096, ENST00000951097, ENST00000951098, ENST00000951099, ENST00000951100, ENST00000951101, ENST00000951102, ENST00000951103, ENST00000951104, ENST00000951105, ENST00000951106, ENST00000951107

RefSeq mRNA: 1 — MANE Select: NM_024541 NM_024541

CCDS: CCDS41563

Canonical transcript exons

ENST00000370033 — 26 exons

Exon	Start	End
ENSE00000811468	101991969	101992038
ENSE00001193232	102033026	102033172
ENSE00001193237	102033283	102033339
ENSE00001193247	102040013	102040125
ENSE00001451560	101993538	101993603
ENSE00001451561	101995297	101995355
ENSE00001451562	102001971	102002072
ENSE00001451563	102006540	102006633
ENSE00001451564	102009374	102009449
ENSE00001451565	102009977	102010023
ENSE00001451566	102011723	102011783
ENSE00001451567	102012833	102012876
ENSE00001451568	102013968	102014024
ENSE00001451569	102023477	102023563
ENSE00001451570	102023675	102023749
ENSE00001451571	102025156	102025248
ENSE00001451572	102029638	102029745
ENSE00002443701	101957650	101957732
ENSE00002444971	101975212	101975300
ENSE00002445529	101956597	101956723
ENSE00002481958	101889412	101889490
ENSE00002503095	101939863	101939938
ENSE00003484237	101845599	101847620
ENSE00003643015	101849776	101849892
ENSE00003784651	101990551	101990611
ENSE00003846824	102056085	102056173

Expression profiles

Bgee: expression breadth ubiquitous, 271 present calls, max score 91.83.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 10.9528 / max 132.1456, expressed in 1789 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
111122	9.7154	1777
111123	1.2027	804
111117	0.0347	15

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
left ventricle myocardium	UBERON:0006566	91.83	gold quality
heart left ventricle	UBERON:0002084	91.73	gold quality
cardiac muscle of right atrium	UBERON:0003379	91.71	gold quality
cardiac ventricle	UBERON:0002082	91.53	gold quality
apex of heart	UBERON:0002098	91.43	gold quality
right atrium auricular region	UBERON:0006631	91.43	gold quality
cardiac atrium	UBERON:0002081	91.40	gold quality
heart	UBERON:0000948	90.22	gold quality
myocardium	UBERON:0002349	89.99	gold quality
monocyte	CL:0000576	89.49	gold quality
mononuclear cell	CL:0000842	89.40	gold quality
tongue squamous epithelium	UBERON:0006919	89.40	silver quality
leukocyte	CL:0000738	89.24	gold quality
lower esophagus mucosa	UBERON:0035834	88.80	gold quality
granulocyte	CL:0000094	88.07	gold quality
gastrocnemius	UBERON:0001388	88.01	gold quality
muscle of leg	UBERON:0001383	87.75	gold quality
mucosa of transverse colon	UBERON:0004991	87.28	gold quality
hindlimb stylopod muscle	UBERON:0004252	87.14	gold quality
gingival epithelium	UBERON:0001949	86.60	gold quality
muscle organ	UBERON:0001630	86.30	gold quality
islet of Langerhans	UBERON:0000006	86.23	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	86.17	gold quality
skin of leg	UBERON:0001511	86.11	gold quality
esophagus mucosa	UBERON:0002469	86.05	gold quality
lower esophagus	UBERON:0013473	85.88	gold quality
lower esophagus muscularis layer	UBERON:0035833	85.87	gold quality
esophagus	UBERON:0001043	85.86	gold quality
muscle layer of sigmoid colon	UBERON:0035805	85.81	gold quality
popliteal artery	UBERON:0002250	85.74	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	5.37

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

107 targeting ARMH3, 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-4692	100.00	67.32	2066
HSA-MIR-30A-5P	100.00	76.31	3233
HSA-MIR-30B-5P	100.00	76.29	3248
HSA-MIR-30C-5P	100.00	76.29	3248
HSA-MIR-30D-5P	100.00	76.32	3233
HSA-MIR-30E-5P	100.00	76.32	3242
HSA-MIR-3925-3P	100.00	69.95	1237
HSA-MIR-6873-3P	100.00	71.42	2626
HSA-MIR-4514	99.99	67.10	1870
HSA-MIR-4715-3P	99.98	66.03	670
HSA-MIR-4267	99.96	66.53	2368
HSA-MIR-146A-5P	99.96	68.93	988
HSA-MIR-146B-5P	99.96	69.13	977
HSA-MIR-185-3P	99.95	67.01	1743
HSA-MIR-7153-5P	99.94	68.89	1006
HSA-MIR-6845-3P	99.94	66.88	1439
HSA-MIR-205-3P	99.92	69.92	3165
HSA-MIR-4739	99.84	65.25	1832
HSA-MIR-4756-5P	99.84	64.98	1809
HSA-MIR-1321	99.84	65.30	1811
HSA-MIR-520F-3P	99.82	71.32	1216
HSA-MIR-1299	99.77	71.24	2389
HSA-MIR-3934-3P	99.76	65.51	1351
HSA-MIR-6764-5P	99.75	67.89	2304
HSA-MIR-6745	99.74	65.33	1321
HSA-MIR-1825	99.72	68.11	1089
HSA-MIR-12124	99.68	69.17	2700
HSA-MIR-5093	99.67	69.26	2291
HSA-MIR-6512-3P	99.65	66.07	1468
HSA-MIR-6720-5P	99.65	66.22	1459

Literature-anchored findings (GeneRIF, showing 1)

• The C10orf76-PI4KB axis orchestrates CERT-mediated ceramide trafficking to the distal Golgi. (PMID:37195633)

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	armh3	ENSDARG00000104285
mus_musculus	Armh3	ENSMUSG00000039901
rattus_norvegicus	Armh3	ENSRNOG00000025523
drosophila_melanogaster	CG8379	FBGN0037638

Protein

Protein identifiers

Armadillo-like helical domain-containing protein 3 — Q5T2E6 (reviewed: Q5T2E6)

All UniProt accessions (3): Q5T2E6, Q5T2E7, Q5T2E8

UniProt curated annotations — full annotation on UniProt →

Function. Involved in GBF1 recruitment, Golgi maintenance and protein secretion.

Subunit / interactions. Interacts with PI4KB. Interacts with GBF1.

Subcellular location. Golgi apparatus membrane. Cytoplasm.

Miscellaneous. May be produced at very low levels due to a premature stop codon in the mRNA, leading to nonsense-mediated mRNA decay.

Similarity. Belongs to the ARMH3 family.

Isoforms (3)

UniProt ID	Names	Canonical?
Q5T2E6-1	1	yes
Q5T2E6-2	2
Q5T2E6-3	3

RefSeq proteins (1): NP_078817* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR013636	ARMH3_C	Domain
IPR016024	ARM-type_fold	Homologous_superfamily
IPR039868	ARMD3-like	Family

Pfam: PF08427

UniProt features (6 total): splice variant 3, chain 1, transmembrane region 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q5T2E6-F1	84.97	0.66

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 119 (showing top): GOBP_REGULATION_OF_GOLGI_ORGANIZATION, GOBP_PROTEIN_ACTIVATION_CASCADE, GOBP_VESICLE_MEDIATED_TRANSPORT, GOBP_PROTEIN_MATURATION, WTGAAAT_UNKNOWN, GOBP_GOLGI_TO_ENDOSOME_TRANSPORT, GOBP_ENDOMEMBRANE_SYSTEM_ORGANIZATION, LASTOWSKA_NEUROBLASTOMA_COPY_NUMBER_DN, TGTTTAC_MIR30A5P_MIR30C_MIR30D_MIR30B_MIR30E5P, IK3_01, XU_GH1_AUTOCRINE_TARGETS_DN, GOBP_RESPONSE_TO_VIRUS, GOBP_CYTOSOLIC_TRANSPORT, GOBP_GOLGI_ORGANIZATION, LIU_SOX4_TARGETS_DN

GO Biological Process (1): regulation of Golgi organization (GO:1903358)

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

GO Cellular Component (5): Golgi membrane (GO:0000139), cytosol (GO:0005829), cytoplasm (GO:0005737), Golgi apparatus (GO:0005794), membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	3
cytoplasm	2
Golgi organization	1
regulation of organelle organization	1
binding	1
Golgi apparatus	1
bounding membrane of organelle	1
intracellular anatomical structure	1
endomembrane system	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

346 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ARMH3	PI4KB	P78405	852
ARMH3	ACBD3	Q9H3P7	722
ARMH3	NOL7	Q9UMY1	562
ARMH3	CNOT10	Q9H9A5	544
ARMH3	TMUB2	Q71RG4	540
ARMH3	AMMECR1L	Q6DCA0	478
ARMH3	TLK2	Q86UE8	452
ARMH3	NUBP1	P53384	451
ARMH3	MTMR14	Q8NCE2	447
ARMH3	SLC4A1AP	Q9BWU0	446
ARMH3	WIPF3	A6NGB9	444
ARMH3	BLOC1S2	Q6QNY1	410
ARMH3	ZKSCAN5	Q9Y2L8	398
ARMH3	ACAD9	Q9H845	389
ARMH3	GBF1	Q92538	370

IntAct

6 interactions, top by confidence:

A	B	Type	Score
ARMH3	PI4KB	psi-mi:“MI:0915”(physical association)	0.370
PI4KB	MTA2	psi-mi:“MI:0914”(association)	0.350
GYPA	HYKK	psi-mi:“MI:0914”(association)	0.350
C3orf18	EXOC5	psi-mi:“MI:0914”(association)	0.350
FASN	ARMH3	psi-mi:“MI:0914”(association)	0.350

BioGRID (38): C10orf76 (Affinity Capture-RNA), C10orf76 (Affinity Capture-RNA), C10orf76 (Affinity Capture-RNA), C10orf76 (Co-fractionation), CLASP2 (Synthetic Lethality), PTPN23 (Synthetic Lethality), UBAP1 (Synthetic Lethality), TSSC1 (Synthetic Lethality), C10orf76 (Synthetic Lethality), C10orf76 (Synthetic Lethality), COG8 (Synthetic Lethality), RIC1 (Synthetic Lethality), COG3 (Synthetic Lethality), COG7 (Synthetic Lethality), VPS53 (Synthetic Lethality)

ESM2 similar proteins: A0JNG7, A0JPF5, A0JPG1, A2VE70, B4F766, O70481, P50851, Q05DH4, Q08AM6, Q0P4Q0, Q0VGW0, Q15173, Q28BM0, Q293C2, Q3UHQ6, Q4S6U8, Q5RAW5, Q5SP90, Q5T2E6, Q5W0V3, Q5ZIW5, Q5ZLW3, Q68F38, Q68F70, Q6DCP6, Q6DCT2, Q6GPP1, Q6INN7, Q6PD19, Q6PGW3, Q6ZS30, Q7KNA0, Q7RTS9, Q80TR8, Q80W92, Q80WQ2, Q80YR2, Q86V87, Q8CDM8, Q8CHY3

Diamond homologs: Q5T2E6, Q6DCT2, Q6PD19, Q6PGW3

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

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

Top pathogenic / likely-pathogenic (0)

SpliceAI

5300 predictions. Top by Δscore:

Variant	Effect	Δscore
10:101848399:CT:C	donor_gain	1.0000
10:101849771:CTCA:C	donor_loss	1.0000
10:101849772:TCA:T	donor_loss	1.0000
10:101849773:CAC:C	donor_loss	1.0000
10:101849774:A:AC	donor_gain	1.0000
10:101849774:A:C	donor_loss	1.0000
10:101849774:AC:A	donor_gain	1.0000
10:101849774:ACCAG:A	donor_gain	1.0000
10:101849775:C:CT	donor_gain	1.0000
10:101849775:CC:C	donor_gain	1.0000
10:101849775:CCA:C	donor_gain	1.0000
10:101849775:CCAG:C	donor_gain	1.0000
10:101849775:CCAGC:C	donor_gain	1.0000
10:101849798:T:TA	donor_gain	1.0000
10:101849891:ACCT:A	acceptor_loss	1.0000
10:101849894:T:A	acceptor_loss	1.0000
10:101939934:CAGGA:C	acceptor_gain	1.0000
10:101939939:C:CC	acceptor_gain	1.0000
10:101955540:T:A	donor_gain	1.0000
10:101955544:C:CA	donor_gain	1.0000
10:101956591:GCTTA:G	donor_loss	1.0000
10:101956592:CTTAC:C	donor_loss	1.0000
10:101956593:TTACC:T	donor_loss	1.0000
10:101956594:TA:T	donor_loss	1.0000
10:101956595:A:AC	donor_gain	1.0000
10:101956595:AC:A	donor_gain	1.0000
10:101956596:C:CC	donor_gain	1.0000
10:101956596:C:CT	donor_loss	1.0000
10:101956596:CC:C	donor_gain	1.0000
10:101956720:CAAT:C	acceptor_gain	1.0000

AlphaMissense

4591 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
10:101849852:A:G	L634P	1.000
10:101849852:A:T	L634Q	1.000
10:101849858:A:G	L632P	1.000
10:101849858:A:T	L632H	1.000
10:101889477:G:C	H599D	1.000
10:101939868:A:C	N592K	1.000
10:101939868:A:T	N592K	1.000
10:101956632:C:G	R557P	1.000
10:101956650:A:G	L551P	1.000
10:101956677:A:G	L542P	1.000
10:101956686:T:A	D539V	1.000
10:101956687:C:G	D539H	1.000
10:101956689:C:A	G538V	1.000
10:101956689:C:T	G538D	1.000
10:101956690:C:A	G538C	1.000
10:101956690:C:G	G538R	1.000
10:101975218:A:G	W497R	1.000
10:101975218:A:T	W497R	1.000
10:101975230:A:G	W493R	1.000
10:101975230:A:T	W493R	1.000
10:101990608:A:G	L450P	1.000
10:102009401:A:C	N309K	1.000
10:102009401:A:T	N309K	1.000
10:102013999:A:G	L232P	1.000
10:102014016:A:C	N226K	1.000
10:102014016:A:T	N226K	1.000
10:102014018:T:C	N226D	1.000
10:102023487:C:A	R220I	1.000
10:102023726:G:C	N177K	1.000
10:102023726:G:T	N177K	1.000

dbSNP variants (sampled 300 via entrez): RS1000029857 (10:101971304 C>T), RS1000060749 (10:101912249 C>T), RS1000061344 (10:101958126 C>T), RS1000061739 (10:102026111 T>C), RS1000075626 (10:102045211 T>C), RS1000101568 (10:101971668 G>A), RS1000102581 (10:101926662 C>T), RS1000108329 (10:101880166 A>C,G), RS1000110579 (10:102001367 C>T), RS1000139574 (10:102008719 T>C), RS1000141850 (10:101864737 C>T), RS1000156008 (10:101849415 T>C), RS1000193628 (10:101994936 C>A,T), RS1000218002 (10:101994647 C>A), RS1000224944 (10:101951023 C>T)

Disease associations

OMIM: gene MIM:620867 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

12 associations (top):

Study	Trait	p-value
GCST002097_2	Coronary artery calcification	4.000000e-06
GCST005141_70	Cognitive ability (MTAG)	3.000000e-09
GCST005316_350	Intelligence (MTAG)	4.000000e-08
GCST005316_458	Intelligence (MTAG)	4.000000e-09
GCST005316_71	Intelligence (MTAG)	1.000000e-16
GCST005316_75	Intelligence (MTAG)	5.000000e-09
GCST006061_107	Atrial fibrillation	1.000000e-09
GCST006269_613	General cognitive ability	7.000000e-13
GCST006626_5	Pulse pressure	3.000000e-13
GCST009524_144	Household income (MTAG)	9.000000e-13
GCST009524_264	Household income (MTAG)	5.000000e-11
GCST010138_11	Raw vegetable consumption	3.000000e-08

EFO canonical traits (6, from GWAS)

EFO ID	Trait name
EFO:0004723	coronary artery calcification
EFO:0004337	intelligence
EFO:0004784	self reported educational attainment
EFO:0005763	pulse pressure measurement
EFO:0009695	household income
EFO:0008111	diet measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

18 total (human), top 18 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Arsenic	affects expression, affects cotreatment, decreases expression, increases abundance	2
Valproic Acid	increases expression, decreases expression	2
aristolochic acid I	decreases expression	1
bisphenol A	decreases methylation	1
trichostatin A	decreases expression	1
tris(1,3-dichloro-2-propyl)phosphate	increases expression	1
sodium arsenite	affects cotreatment, decreases expression, increases abundance	1
manganese chloride	affects cotreatment, decreases expression, increases abundance	1
Resveratrol	affects cotreatment, increases expression	1
Benzo(a)pyrene	affects methylation	1
Doxorubicin	decreases expression	1
Hydrogen Peroxide	decreases expression	1
Manganese	decreases expression, increases abundance, affects cotreatment	1
Methyl Methanesulfonate	increases expression	1
Plant Extracts	affects cotreatment, increases expression	1
Rotenone	decreases expression	1
Tobacco Smoke Pollution	increases expression	1
Lactic Acid	decreases expression	1

Clinical trials (associated diseases)

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