ARMC7

Summary

ARMC7 (armadillo repeat containing 7, HGNC:26168) is a protein-coding gene on chromosome 17q25.1, encoding Armadillo repeat-containing protein 7 (Q9H6L4). As a component of the minor spliceosome, involved in the splicing of U12-type introns in pre-mRNAs. It is a common-essential gene (DepMap: required in 97.3% of cancer cell lines).

Predicted to be involved in RNA splicing and mRNA processing. Predicted to be part of spliceosomal complex.

Source: NCBI Gene 79637 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 43 total — 1 pathogenic
• Cancer dependency (DepMap): dependent in 97.3% of screened cell lines (common-essential)
• MANE Select transcript: NM_024585

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:26168
Approved symbol	ARMC7
Name	armadillo repeat containing 7
Location	17q25.1
Locus type	gene with protein product
Status	Approved
Aliases	FLJ22160
Ensembl gene	ENSG00000125449
Ensembl biotype	protein_coding
Entrez	79637

Gene structure

Transcript identifiers

Ensembl transcripts: 6 — 5 protein_coding, 1 protein_coding_CDS_not_defined

ENST00000245543, ENST00000579096, ENST00000581078, ENST00000582136, ENST00000584947, ENST00000954034

RefSeq mRNA: 4 — MANE Select: NM_024585 NM_001304271, NM_001304272, NM_001304273, NM_024585

CCDS: CCDS11714, CCDS77107, CCDS77108, CCDS77109

Canonical transcript exons

ENST00000245543 — 3 exons

Exon	Start	End
ENSE00000855659	75110463	75110606
ENSE00001174834	75128677	75130272
ENSE00001196416	75109969	75110379

Expression profiles

Bgee: expression breadth ubiquitous, 278 present calls, max score 93.10.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 10.9348 / max 152.9079, expressed in 1762 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
162703	8.4363	1740
162704	2.1280	1072
208376	0.3706	202

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
triceps brachii	UBERON:0001509	93.10	silver quality
metanephros cortex	UBERON:0010533	91.73	gold quality
type B pancreatic cell	CL:0000169	90.85	silver quality
olfactory bulb	UBERON:0002264	90.76	silver quality
gluteal muscle	UBERON:0002000	90.47	silver quality
mucosa of transverse colon	UBERON:0004991	89.60	gold quality
pancreatic ductal cell	CL:0002079	89.40	gold quality
adult mammalian kidney	UBERON:0000082	85.57	gold quality
blood	UBERON:0000178	84.73	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	84.71	gold quality
granulocyte	CL:0000094	84.44	gold quality
male germ cell	CL:0000015	83.06	silver quality
cerebellar hemisphere	UBERON:0002245	82.58	gold quality
right hemisphere of cerebellum	UBERON:0014890	82.53	gold quality
cerebellar cortex	UBERON:0002129	82.51	gold quality
cerebellum	UBERON:0002037	82.39	gold quality
biceps brachii	UBERON:0001507	82.32	silver quality
sperm	CL:0000019	82.29	silver quality
transverse colon	UBERON:0001157	82.00	gold quality
apex of heart	UBERON:0002098	81.81	gold quality
heart right ventricle	UBERON:0002080	81.74	silver quality
skeletal muscle tissue of biceps brachii	UBERON:0004502	81.72	silver quality
endothelial cell	CL:0000115	81.62	silver quality
leukocyte	CL:0000738	81.61	gold quality
lower esophagus mucosa	UBERON:0035834	81.54	gold quality
upper lobe of left lung	UBERON:0008952	81.50	gold quality
monocyte	CL:0000576	81.28	gold quality
mononuclear cell	CL:0000842	81.27	gold quality
body of stomach	UBERON:0001161	81.00	gold quality
lateral globus pallidus	UBERON:0002476	80.98	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	6.04
E-ENAD-17	no	121.93

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

35 targeting ARMC7, 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-4673	100.00	66.64	1490
HSA-MIR-345-3P	99.89	70.23	1421
HSA-MIR-4319	99.76	69.83	2586
HSA-MIR-6764-5P	99.75	67.89	2304
HSA-MIR-4530	99.69	66.47	1509
HSA-MIR-670-5P	99.67	69.94	1565
HSA-MIR-3175	99.65	66.30	2031
HSA-MIR-9851-3P	99.63	69.68	1110
HSA-MIR-1915-3P	99.58	66.79	1988
HSA-MIR-486-3P	99.51	66.82	1901
HSA-MIR-766-3P	99.47	65.24	1811
HSA-MIR-889-5P	99.41	68.75	1025
HSA-MIR-3182	99.40	68.15	2454
HSA-MIR-125A-5P	99.36	70.59	1640
HSA-MIR-125B-5P	99.36	70.36	1662
HSA-MIR-593-5P	99.34	69.50	965
HSA-MIR-4685-5P	99.25	65.99	1563
HSA-MIR-6837-5P	99.25	65.47	1632
HSA-MIR-6809-5P	99.13	68.45	1223
HSA-MIR-4651	99.06	67.57	2002
HSA-MIR-608	98.93	67.83	2013
HSA-MIR-3074-5P	98.82	66.56	1414
HSA-MIR-432-5P	98.00	68.13	989
HSA-MIR-3198	97.84	65.64	579
HSA-MIR-4309	97.84	65.45	588
HSA-MIR-6893-3P	97.79	64.91	1238
HSA-MIR-3189-5P	97.55	66.71	655
HSA-MIR-4732-3P	97.15	65.45	881
HSA-MIR-370-3P	97.09	64.92	1221
HSA-MIR-1913	97.07	66.20	1417

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 97.3% of screened cell lines, common-essential.

Cross-species orthologs

1 orthologs

Organism	Symbol	Gene ID
mus_musculus	Armc7	ENSMUSG00000057219

Protein

Protein identifiers

Armadillo repeat-containing protein 7 — Q9H6L4 (reviewed: Q9H6L4)

All UniProt accessions (3): Q9H6L4, J3KST7, J3KTE5

UniProt curated annotations — full annotation on UniProt →

Function. As a component of the minor spliceosome, involved in the splicing of U12-type introns in pre-mRNAs.

Subunit / interactions. Component of the minor spliceosome. Within this complex, interacts with RBM48.

Isoforms (2)

UniProt ID	Names	Canonical?
Q9H6L4-1	1	yes
Q9H6L4-2	2

RefSeq proteins (4): NP_001291200, NP_001291201, NP_001291202, NP_078861* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR000225	Armadillo	Repeat
IPR011989	ARM-like	Homologous_superfamily
IPR016024	ARM-type_fold	Homologous_superfamily
IPR042462	ARMC7	Family

Pfam: PF00514

UniProt features (21 total): helix 13, repeat 2, turn 2, splice variant 2, chain 1, modified residue 1

Structure

Experimental structures (PDB)

1 structures.

PDB	Method	Resolution (Å)
7DVQ	ELECTRON MICROSCOPY	2.89

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9H6L4-F1	88.64	0.78

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): 169

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 129 (showing top): GRAESSMANN_APOPTOSIS_BY_SERUM_DEPRIVATION_UP, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_UP, GRAESSMANN_RESPONSE_TO_MC_AND_DOXORUBICIN_UP, MODULE_205, GOBP_RNA_SPLICING, ACEVEDO_LIVER_CANCER_UP, NIKOLSKY_BREAST_CANCER_17Q21_Q25_AMPLICON, GOCC_CATALYTIC_STEP_2_SPLICEOSOME, GOCC_SPLICEOSOMAL_COMPLEX, GOCC_RIBONUCLEOPROTEIN_COMPLEX, SCGGAAGY_ELK1_02, GOCC_U12_TYPE_SPLICEOSOMAL_COMPLEX, CHEN_METABOLIC_SYNDROM_NETWORK, BHAT_ESR1_TARGETS_NOT_VIA_AKT1_DN, GOBP_MRNA_PROCESSING

GO Biological Process (2): mRNA processing (GO:0006397), RNA splicing (GO:0008380)

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

GO Cellular Component (1): spliceosomal complex (GO:0005681)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
RNA processing	2
mRNA metabolic process	1
binding	1
nuclear protein-containing complex	1
ribonucleoprotein complex	1

Protein interactions and networks

STRING

572 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ARMC7	RBM48	Q5RL73	766
ARMC7	ZNF662	Q6ZS27	546
ARMC7	KCTD2	Q14681	527
ARMC7	GASK1A	Q9UFP1	506
ARMC7	TRARG1	Q8IXB3	469
ARMC7	ARMC6	Q6NXE6	459
ARMC7	MAEA	Q7L5Y9	459
ARMC7	ATP5PD	O75947	454
ARMC7	KLHDC4	Q8TBB5	447
ARMC7	DMAC1	Q96GE9	444
ARMC7	NAB2	Q15742	425
ARMC7	INTS2	Q9H0H0	423
ARMC7	SLC16A5	O15375	410
ARMC7	KLF10	Q13118	405
ARMC7	SNRNP35	Q16560	402

IntAct

253 interactions, top by confidence:

A	B	Type	Score
IKZF3	ARMC7	psi-mi:“MI:0915”(physical association)	0.840
ARMC7	IKZF3	psi-mi:“MI:0915”(physical association)	0.840
RBM48	ARMC7	psi-mi:“MI:0915”(physical association)	0.800
TRIM27	ARMC7	psi-mi:“MI:0915”(physical association)	0.720
TNFAIP1	ARMC7	psi-mi:“MI:0915”(physical association)	0.720
KRT31	ARMC7	psi-mi:“MI:0915”(physical association)	0.720
KRT40	ARMC7	psi-mi:“MI:0915”(physical association)	0.720
ARMC7	TRIM27	psi-mi:“MI:0915”(physical association)	0.720
ARMC7	KRT31	psi-mi:“MI:0915”(physical association)	0.720
ARMC7	TNFAIP1	psi-mi:“MI:0915”(physical association)	0.720
ARMC7	CPSF6	psi-mi:“MI:0915”(physical association)	0.670
ABI2	ARMC7	psi-mi:“MI:0915”(physical association)	0.670
ARMC7	ABI2	psi-mi:“MI:0915”(physical association)	0.670

BioGRID (107): ARMC7 (Two-hybrid), ARMC7 (Two-hybrid), ARMC7 (Two-hybrid), ARMC7 (Two-hybrid), ARMC7 (Two-hybrid), ARMC7 (Two-hybrid), ARMC7 (Two-hybrid), ARMC7 (Two-hybrid), ARMC7 (Two-hybrid), ARMC7 (Two-hybrid), ARMC7 (Two-hybrid), CPSF7 (Two-hybrid), CCDC33 (Two-hybrid), EFHC2 (Two-hybrid), SPATC1L (Two-hybrid)

ESM2 similar proteins: A0A8I5ZNK2, A1L1L6, A2VE08, B0R0D7, F1QGH7, F1QH17, O15131, O35116, O35142, O35345, O55029, O60684, O60763, O95782, P14685, P17426, P26233, P31016, P35224, P35605, P35606, P41541, P41542, P52294, P70188, P78352, P83953, Q0V7M0, Q2HJF8, Q2KJ46, Q4R4I8, Q503E9, Q56R16, Q5NVK4, Q5R664, Q5R909, Q5RBV0, Q5ZM83, Q5ZML1, Q60960

Diamond homologs: Q3UJZ3, Q9H6L4

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 69 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

Pathway	Partners	Fold	FDR
Formation of the cornified envelope	5	11.0×	7e-03
Keratinization	7	9.8×	1e-03

GO biological processes:

GO term	Partners	Fold	FDR
intermediate filament organization	6	22.9×	8e-05

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	1
Likely pathogenic	0
Uncertain significance	37
Likely benign	4
Benign	0

Top pathogenic / likely-pathogenic (1)

Variant ID	HGVS	Classification
625759	GRCh37/hg19 17q24.3-25.1(chr17:70720436-73175266)	Pathogenic

SpliceAI

504 predictions. Top by Δscore:

Variant	Effect	Δscore
17:75110605:TGGTA:T	donor_loss	1.0000
17:75110607:G:GG	donor_gain	1.0000
17:75110607:GT:G	donor_loss	1.0000
17:75110608:T:A	donor_loss	1.0000
17:75114283:G:GT	donor_gain	1.0000
17:75128674:CA:C	acceptor_loss	1.0000
17:75128675:A:AG	acceptor_gain	1.0000
17:75128676:G:GG	acceptor_gain	1.0000
17:75128676:GGA:G	acceptor_gain	1.0000
17:75110376:CAAGG:C	donor_loss	0.9900
17:75110377:AAGG:A	donor_loss	0.9900
17:75110378:AGGTG:A	donor_loss	0.9900
17:75110379:GGTGA:G	donor_loss	0.9900
17:75110380:G:C	donor_loss	0.9900
17:75110381:T:G	donor_loss	0.9900
17:75110461:A:AG	acceptor_gain	0.9900
17:75110462:G:GG	acceptor_gain	0.9900
17:75110462:GAC:G	acceptor_gain	0.9900
17:75110576:GAGAA:G	donor_gain	0.9900
17:75110592:TG:T	donor_gain	0.9900
17:75110593:GG:G	donor_gain	0.9900
17:75110603:ATTG:A	donor_gain	0.9900
17:75110604:TTG:T	donor_gain	0.9900
17:75110605:TG:T	donor_gain	0.9900
17:75110606:GG:G	donor_gain	0.9900
17:75114357:G:GT	donor_gain	0.9900
17:75128675:AG:A	acceptor_gain	0.9900
17:75128675:AGGAG:A	acceptor_gain	0.9900
17:75128676:GG:G	acceptor_gain	0.9900
17:75128676:GGAGG:G	acceptor_gain	0.9900

AlphaMissense

1277 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
17:75110490:T:C	L40P	0.996
17:75128680:G:A	G80D	0.996
17:75110490:T:A	L40H	0.995
17:75110498:T:C	F43L	0.995
17:75110500:C:A	F43L	0.995
17:75110500:C:G	F43L	0.995
17:75110502:C:A	A44D	0.995
17:75110601:C:A	A77D	0.994
17:75110497:C:A	N42K	0.993
17:75110497:C:G	N42K	0.993
17:75128679:G:C	G80R	0.993
17:75110358:T:C	F24L	0.991
17:75110360:C:A	F24L	0.991
17:75110360:C:G	F24L	0.991
17:75110481:T:C	L37P	0.991
17:75128794:C:A	A118D	0.991
17:75128920:C:A	A160E	0.991
17:75110501:G:C	A44P	0.989
17:75110556:T:C	F62S	0.989
17:75128793:G:C	A118P	0.989
17:75110484:C:A	A38D	0.988
17:75110492:G:C	A41P	0.987
17:75110493:C:A	A41D	0.987
17:75110499:T:C	F43S	0.987
17:75110597:T:C	F76L	0.987
17:75110599:T:A	F76L	0.987
17:75110599:T:G	F76L	0.987
17:75128692:T:C	L84P	0.987
17:75110347:T:C	L20P	0.986
17:75110350:T:A	V21D	0.986

dbSNP variants (sampled 300 via entrez): RS1000015816 (17:75129287 G>C,T), RS1000076548 (17:75118520 C>T), RS1000143309 (17:75108020 CTT>C), RS1000249494 (17:75128051 T>A,C), RS1000256299 (17:75124305 G>A,T), RS1000329702 (17:75113512 G>C), RS1000386360 (17:75118800 A>G), RS1000452930 (17:75108280 C>G), RS1000673173 (17:75120170 G>A,T), RS1000706418 (17:75128284 G>C,T), RS1000956805 (17:75115215 G>C), RS1000997420 (17:75125446 A>G), RS1001074929 (17:75114890 C>T), RS1001342669 (17:75113334 A>AT), RS1001472602 (17:75127525 C>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

1 associations (top):

Study	Trait	p-value
GCST008103_113	Bipolar disorder	4.000000e-06

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

27 total (human), top 27 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
aristolochic acid I	increases expression	1
triphenyl phosphate	affects expression	1
mono-(2-ethylhexyl)phthalate	increases abundance, increases methylation	1
sodium arsenite	decreases expression	1
ferrous chloride	decreases expression	1
beta-methylcholine	affects expression	1
di-n-butylphosphoric acid	affects expression	1
ICG 001	increases expression	1
2-methyl-2H-pyrazole-3-carboxylic acid (2-methyl-4-o-tolylazophenyl)amide	decreases reaction, decreases expression	1
Resveratrol	affects cotreatment, decreases expression	1
Temozolomide	increases expression	1
Leflunomide	decreases expression	1
Atrazine	decreases expression	1
Vehicle Emissions	decreases expression, decreases reaction	1
Calcitriol	increases expression, affects cotreatment	1
Diethylhexyl Phthalate	increases abundance, increases methylation	1
Doxorubicin	decreases expression	1
Hydrogen Peroxide	decreases expression	1
Methyl Methanesulfonate	increases expression	1
Plant Extracts	affects cotreatment, decreases expression	1
Smoke	decreases expression	1
Testosterone	affects cotreatment, increases expression	1
Thimerosal	decreases expression	1
Thiram	decreases expression	1
Urethane	increases expression	1
Copper Sulfate	decreases expression	1
Particulate Matter	decreases expression, decreases reaction	1

Clinical trials (associated diseases)

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