ARMC1

Summary

ARMC1 (armadillo repeat containing 1, HGNC:17684) is a protein-coding gene on chromosome 8q13.1, encoding Armadillo repeat-containing protein 1 (Q9NVT9). In association with mitochondrial contact site and cristae organizing system (MICOS) complex components and mitochondrial outer membrane sorting assembly machinery (SAM) complex components may regulate mitochondrial dynamics playing a role in determining mitochondrial length, di….

Predicted to enable metal ion binding activity. Involved in intracellular distribution of mitochondria. Located in cytosol and mitochondrion.

Source: NCBI Gene 55156 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 49 total
• MANE Select transcript: NM_018120

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:17684
Approved symbol	ARMC1
Name	armadillo repeat containing 1
Location	8q13.1
Locus type	gene with protein product
Status	Approved
Aliases	FLJ10511, Arcp
Ensembl gene	ENSG00000104442
Ensembl biotype	protein_coding
OMIM	620385
Entrez	55156

Gene structure

Transcript identifiers

Ensembl transcripts: 15 — 13 protein_coding, 1 protein_coding_CDS_not_defined, 1 nonsense_mediated_decay

ENST00000276569, ENST00000458464, ENST00000518908, ENST00000519352, ENST00000523384, ENST00000528721, ENST00000890414, ENST00000890415, ENST00000890416, ENST00000890417, ENST00000939403, ENST00000971599, ENST00000971600, ENST00000971601, ENST00000971602

RefSeq mRNA: 2 — MANE Select: NM_018120 NM_001286702, NM_018120

CCDS: CCDS6181, CCDS69490

Canonical transcript exons

ENST00000276569 — 7 exons

Exon	Start	End
ENSE00001241958	65613244	65613433
ENSE00002139241	65633998	65634177
ENSE00003507540	65627216	65627433
ENSE00003569276	65602458	65604585
ENSE00003591304	65605263	65605337
ENSE00003615622	65605422	65605538
ENSE00003630821	65622263	65622354

Expression profiles

Bgee: expression breadth ubiquitous, 285 present calls, max score 99.73.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 24.9185 / max 221.5980, expressed in 1809 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
93351	23.0437	1808
93352	1.6177	1034
93350	0.2570	106

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
secondary oocyte	CL:0000655	99.73	gold quality
oocyte	CL:0000023	99.38	gold quality
inferior vagus X ganglion	UBERON:0005363	95.53	gold quality
parietal lobe	UBERON:0001872	95.12	gold quality
postcentral gyrus	UBERON:0002581	95.05	gold quality
cerebellar vermis	UBERON:0004720	95.02	gold quality
biceps brachii	UBERON:0001507	94.98	gold quality
pons	UBERON:0000988	94.69	gold quality
skeletal muscle tissue of biceps brachii	UBERON:0004502	94.65	gold quality
cauda epididymis	UBERON:0004360	94.61	gold quality
lateral globus pallidus	UBERON:0002476	94.59	gold quality
caput epididymis	UBERON:0004358	94.59	gold quality
superior vestibular nucleus	UBERON:0007227	94.37	gold quality
jejunal mucosa	UBERON:0000399	94.34	gold quality
subthalamic nucleus	UBERON:0001906	94.15	gold quality
ventral tegmental area	UBERON:0002691	94.15	gold quality
lateral nuclear group of thalamus	UBERON:0002736	94.11	gold quality
skeletal muscle tissue of rectus abdominis	UBERON:0004511	93.78	gold quality
corpus epididymis	UBERON:0004359	93.72	gold quality
jejunum	UBERON:0002115	93.70	gold quality
mucosa of paranasal sinus	UBERON:0005030	93.18	gold quality
ganglionic eminence	UBERON:0004023	93.11	gold quality
substantia nigra pars compacta	UBERON:0001965	93.07	gold quality
lower lobe of lung	UBERON:0008949	93.06	gold quality
cortical plate	UBERON:0005343	92.96	gold quality
oral cavity	UBERON:0000167	92.88	gold quality
heart right ventricle	UBERON:0002080	92.87	gold quality
entorhinal cortex	UBERON:0002728	92.85	gold quality
substantia nigra pars reticulata	UBERON:0001966	92.75	gold quality
superior frontal gyrus	UBERON:0002661	92.74	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

121 targeting ARMC1, 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-3646	100.00	73.56	5283
HSA-MIR-3163	100.00	77.23	8605
HSA-MIR-4795-3P	100.00	74.62	4024
HSA-MIR-3924	100.00	72.09	2394
HSA-MIR-548AW	99.99	72.57	3559
HSA-MIR-3662	99.99	73.82	5684
HSA-MIR-103A-3P	99.98	69.14	1595
HSA-MIR-107	99.98	69.14	1595
HSA-MIR-32-5P	99.98	75.21	1964
HSA-MIR-92A-3P	99.98	75.21	1960
HSA-MIR-92B-3P	99.98	75.25	1955
HSA-MIR-25-3P	99.98	74.60	1817
HSA-MIR-363-3P	99.98	74.72	1821
HSA-MIR-367-3P	99.98	74.83	1819
HSA-MIR-433-3P	99.98	69.37	1203
HSA-MIR-4775	99.98	75.00	6394
HSA-MIR-548AN	99.97	70.91	2817
HSA-MIR-607	99.97	73.62	5593
HSA-MIR-1468-3P	99.96	72.74	3797
HSA-MIR-570-3P	99.96	72.41	4910
HSA-MIR-548AJ-3P	99.96	73.38	5345
HSA-MIR-548X-3P	99.96	73.38	5345
HSA-MIR-590-3P	99.96	74.34	6478
HSA-MIR-23A-3P	99.95	74.24	3163
HSA-MIR-23B-3P	99.95	74.24	3163
HSA-MIR-23C	99.95	73.92	3192
HSA-MIR-548J-3P	99.94	72.61	4881
HSA-MIR-335-3P	99.93	73.36	4958
HSA-MIR-6835-3P	99.93	70.49	2904
HSA-MIR-4760-3P	99.93	70.50	2385

Literature-anchored findings (GeneRIF, showing 1)

• ArmC1 represents therefore a peripheral MICOS/MIB component that appears to play a role in mitochondrial distribution in the cell. (PMID:31644573)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	armc1	ENSDARG00000013861
mus_musculus	Armc1	ENSMUSG00000027599
rattus_norvegicus	Armc1	ENSRNOG00000013253

Protein

Protein identifiers

Armadillo repeat-containing protein 1 — Q9NVT9 (reviewed: Q9NVT9)

All UniProt accessions (4): Q9NVT9, E5RHK3, E5RJ86, E9PR92

UniProt curated annotations — full annotation on UniProt →

Function. In association with mitochondrial contact site and cristae organizing system (MICOS) complex components and mitochondrial outer membrane sorting assembly machinery (SAM) complex components may regulate mitochondrial dynamics playing a role in determining mitochondrial length, distribution and motility.

Subunit / interactions. Interacts with mitochondrial contact site and cristae organizing system (MICOS) complex components IMMT/MIC60 and MICOS10/MIC10. Interacts with mitochondrial outer membrane sorting assembly machinery (SAM) complex components SAMM50 and MTX1.

Subcellular location. Cytoplasm. Mitochondrion. Mitochondrion outer membrane.

Isoforms (2)

UniProt ID	Names	Canonical?
Q9NVT9-1	1	yes
Q9NVT9-2	2

RefSeq proteins (2): NP_001273631, NP_060590* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR000225	Armadillo	Repeat
IPR011989	ARM-like	Homologous_superfamily
IPR016024	ARM-type_fold	Homologous_superfamily
IPR016617	ARMC1	Family
IPR036163	HMA_dom_sf	Homologous_superfamily

Pfam: PF00514

UniProt features (12 total): modified residue 6, splice variant 2, chain 1, repeat 1, region of interest 1, compositionally biased region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9NVT9-F1	78.47	0.58

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 (6): 1, 137, 189, 246, 260, 267

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 178 (showing top): GSE18804_SPLEEN_MACROPHAGE_VS_BRAIN_TUMORAL_MACROPHAGE_DN, GSE45365_CTRL_VS_MCMV_INFECTION_NK_CELL_DN, PATIL_LIVER_CANCER, GTGCCTT_MIR506, ONKEN_UVEAL_MELANOMA_UP, MILI_PSEUDOPODIA_HAPTOTAXIS_UP, GOCC_MITOCHONDRIAL_ENVELOPE, DODD_NASOPHARYNGEAL_CARCINOMA_UP, DING_LUNG_CANCER_EXPRESSION_BY_COPY_NUMBER, GOBP_MITOCHONDRION_LOCALIZATION, GRYDER_PAX3FOXO1_ENHANCERS_IN_TADS, GOBP_ORGANELLE_LOCALIZATION, GOBP_MITOCHONDRION_DISTRIBUTION, NKX3A_01, chr8q13

GO Biological Process (1): intracellular distribution of mitochondria (GO:0048312)

GO Molecular Function (2): metal ion binding (GO:0046872), protein binding (GO:0005515)

GO Cellular Component (5): mitochondrion (GO:0005739), mitochondrial outer membrane (GO:0005741), cytosol (GO:0005829), cytoplasm (GO:0005737), membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	3
cytoplasm	2
mitochondrion distribution	1
cation binding	1
binding	1
intracellular membrane-bounded organelle	1
mitochondrial membrane	1
organelle outer membrane	1
intracellular anatomical structure	1

Protein interactions and networks

STRING

1080 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ARMC1	ARMC12	Q5T9G4	587
ARMC1	MICOS13	Q5XKP0	584
ARMC1	APOOL	Q6UXV4	582
ARMC1	MTX2	O75431	558
ARMC1	RMDN1	Q96DB5	550
ARMC1	FAM151B	Q6UXP7	515
ARMC1	TMEM70	Q9BUB7	469
ARMC1	VCPIP1	Q96JH7	464
ARMC1	ODAD2	Q5T2S8	443
ARMC1	DNAJC11	Q9NVH1	436
ARMC1	MRPL13	Q9BYD1	434
ARMC1	DMTF1	Q9Y222	433
ARMC1	FAM91A1	Q658Y4	418
ARMC1	ELOC	Q15369	409
ARMC1	RIMS2	Q9UQ26	408

IntAct

29 interactions, top by confidence:

A	B	Type	Score
ARMC1	MTFR1L	psi-mi:“MI:0915”(physical association)	0.780
MTFR1L	ARMC1	psi-mi:“MI:0915”(physical association)	0.780
ARMC1	DNAJC11	psi-mi:“MI:0915”(physical association)	0.670
ARMC1	RNF24	psi-mi:“MI:0915”(physical association)	0.560
BAG2	HGS	psi-mi:“MI:0914”(association)	0.530
HSPA2	DNAJC13	psi-mi:“MI:0914”(association)	0.530
HTRA2	HAX1	psi-mi:“MI:2364”(proximity)	0.420
EPS8	ARMC1	psi-mi:“MI:0915”(physical association)	0.370
HSPA8	PPP6C	psi-mi:“MI:0914”(association)	0.350
ARMC1	GNAO1	psi-mi:“MI:0914”(association)	0.350
Dnajc11	DDX3X	psi-mi:“MI:0914”(association)	0.350
Dnajc11	RPN1	psi-mi:“MI:0914”(association)	0.350
DNAJC11	VCP	psi-mi:“MI:0914”(association)	0.350
hspa1a_hspa1b_human-1	SHTN1	psi-mi:“MI:0914”(association)	0.350
ARMC1	DCX	psi-mi:“MI:0914”(association)	0.350
HSPA8	SBNO1	psi-mi:“MI:0914”(association)	0.350
HSPBP1	HGS	psi-mi:“MI:0914”(association)	0.350
MTCH2	IPO5	psi-mi:“MI:0914”(association)	0.350
HSPA8	PLEKHG3	psi-mi:“MI:0914”(association)	0.350
CFTR	UBA6	psi-mi:“MI:2364”(proximity)	0.270
ARMC1	RNF24	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (118): MTFR1L (Two-hybrid), CRMP1 (Affinity Capture-MS), DPYSL3 (Affinity Capture-MS), DPYSL2 (Affinity Capture-MS), STXBP1 (Affinity Capture-MS), ATP4A (Affinity Capture-MS), DPYSL5 (Affinity Capture-MS), CAMK2A (Affinity Capture-MS), CAMK2B (Affinity Capture-MS), DNAJC11 (Affinity Capture-MS), GPM6B (Affinity Capture-MS), HIST1H2BL (Affinity Capture-MS), VSNL1 (Affinity Capture-MS), NCAM1 (Affinity Capture-MS), EPB41L1 (Affinity Capture-MS)

ESM2 similar proteins: A4FUD6, A4QNE0, B5KFI0, F1Q8X5, O35841, P40763, P42224, P42227, P52631, P70398, Q19S50, Q3ZBE1, Q5R644, Q5R8I6, Q5R8N4, Q5RCC1, Q5RCR8, Q5XI83, Q6DFZ1, Q6DV79, Q6NRC7, Q6NRL4, Q6QI06, Q6R327, Q7SXV1, Q7Z3J2, Q8BHL5, Q8BIK4, Q8BPU7, Q8BWQ6, Q8CIB5, Q8CIQ7, Q8IWV8, Q8IWZ6, Q8IZD9, Q8K0F1, Q8K2G4, Q8R5L3, Q924Z6, Q92538

Diamond homologs: Q3ZBE1, Q5RCR8, Q5ZMQ0, Q9D7A8, Q9NVT9

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	34
Likely benign	1
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1069 predictions. Top by Δscore:

Variant	Effect	Δscore
8:65604583:CAT:C	acceptor_gain	1.0000
8:65604586:C:CA	acceptor_loss	1.0000
8:65604589:A:AC	acceptor_gain	1.0000
8:65604592:C:CT	acceptor_gain	1.0000
8:65604593:A:T	acceptor_gain	1.0000
8:65605255:A:C	donor_gain	1.0000
8:65605257:TTTTA:T	donor_loss	1.0000
8:65605258:TTTA:T	donor_loss	1.0000
8:65605259:TTAC:T	donor_loss	1.0000
8:65605260:TACCT:T	donor_loss	1.0000
8:65605261:ACC:A	donor_loss	1.0000
8:65605262:CCT:C	donor_gain	1.0000
8:65605336:GC:G	acceptor_gain	1.0000
8:65605337:CC:C	acceptor_gain	1.0000
8:65605337:CCTAA:C	acceptor_loss	1.0000
8:65605338:C:CC	acceptor_gain	1.0000
8:65605338:CTAAG:C	acceptor_loss	1.0000
8:65605339:T:C	acceptor_loss	1.0000
8:65605344:C:CT	acceptor_gain	1.0000
8:65605345:A:T	acceptor_gain	1.0000
8:65605416:ACTT:A	donor_loss	1.0000
8:65605419:TA:T	donor_loss	1.0000
8:65605420:A:AC	donor_gain	1.0000
8:65605421:C:CC	donor_gain	1.0000
8:65605421:CCT:C	donor_gain	1.0000
8:65605421:CCTCA:C	donor_gain	1.0000
8:65605534:CGAGA:C	acceptor_gain	1.0000
8:65605535:GAGA:G	acceptor_gain	1.0000
8:65605535:GAGAC:G	acceptor_loss	1.0000
8:65605536:AGAC:A	acceptor_loss	1.0000

AlphaMissense

1843 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
8:65604399:A:G	W282R	1.000
8:65604399:A:T	W282R	1.000
8:65604416:A:G	L276S	1.000
8:65604428:G:T	A272D	1.000
8:65604441:A:G	W268R	1.000
8:65604441:A:T	W268R	1.000
8:65605288:A:T	V211D	1.000
8:65605321:A:T	I200K	1.000
8:65605333:A:G	L196S	1.000
8:65605447:C:G	R186P	1.000
8:65605450:A:T	V185E	1.000
8:65605455:A:C	C183W	1.000
8:65605456:C:T	C183Y	1.000
8:65605457:A:G	C183R	1.000
8:65605476:A:C	F176L	1.000
8:65605476:A:T	F176L	1.000
8:65605478:A:G	F176L	1.000
8:65605483:A:G	F174S	1.000
8:65605485:G:C	S173R	1.000
8:65605485:G:T	S173R	1.000
8:65605486:C:T	S173N	1.000
8:65605487:T:G	S173R	1.000
8:65605489:A:C	I172S	1.000
8:65605489:A:T	I172N	1.000
8:65605492:A:T	V171D	1.000
8:65605495:C:A	G170V	1.000
8:65605496:C:A	G170C	1.000
8:65605496:C:G	G170R	1.000
8:65605510:A:G	L165S	1.000
8:65613254:A:G	L152P	1.000

dbSNP variants (sampled 300 via entrez): RS1000137589 (8:65616252 C>T), RS1000170801 (8:65616361 C>T), RS1000184683 (8:65602110 T>G), RS1000222022 (8:65627468 G>A), RS1000378783 (8:65623901 G>A), RS1000401312 (8:65634766 A>G), RS1000477303 (8:65615163 T>A), RS1000478382 (8:65630516 C>T), RS1000556428 (8:65615444 C>A,T), RS1000642022 (8:65610390 C>T), RS1000654913 (8:65621991 G>A), RS1000707202 (8:65621702 T>G), RS1000728806 (8:65624282 T>C), RS1000748829 (8:65603265 T>C), RS1000778936 (8:65628750 G>A)

Disease associations

OMIM: gene MIM:620385 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

1 associations (top):

Study	Trait	p-value
GCST001762_218	Obesity-related traits	8.000000e-06

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

26 total (human), top 26 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
bisphenol A	decreases expression	2
aristolochic acid I	decreases expression	1
dicrotophos	decreases expression	1
triphenyl phosphate	affects expression	1
beta-lapachone	increases expression	1
sodium arsenite	decreases expression	1
perfluorooctanoic acid	increases expression	1
potassium chromate(VI)	affects cotreatment, decreases expression	1
coumarin	decreases phosphorylation	1
beta-methylcholine	affects expression	1
epigallocatechin gallate	affects cotreatment, decreases expression	1
di-n-butylphosphoric acid	affects expression	1
ICG 001	increases expression	1
Resveratrol	affects cotreatment, increases expression	1
Sunitinib	increases expression	1
Air Pollutants	decreases expression, increases abundance	1
Cadmium	decreases expression	1
Caffeine	decreases phosphorylation	1
Diethylstilbestrol	decreases expression	1
Ivermectin	decreases expression	1
Plant Extracts	affects cotreatment, increases expression	1
Tretinoin	decreases expression	1
Valproic Acid	increases expression	1
Antirheumatic Agents	increases expression	1
Copper Sulfate	decreases expression	1
Particulate Matter	decreases expression, increases abundance	1

Clinical trials (associated diseases)

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