ARMCX4

Summary

ARMCX4 (armadillo repeat containing X-linked 4, HGNC:28615) is a protein-coding gene on chromosome Xq22.1, encoding Armadillo repeat-containing X-linked protein 4 (Q5H9R4).

The product of this gene belongs to the armadillo repeat-containing family of proteins, which interact with other proteins in a variety of cellular processes. The function of this family member is currently unknown. Alternative splicing of this gene results in multiple transcript variants.

Source: NCBI Gene 100131755 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 17 total
• MANE Select transcript: NM_001256155

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:28615
Approved symbol	ARMCX4
Name	armadillo repeat containing X-linked 4
Location	Xq22.1
Locus type	gene with protein product
Status	Approved
Aliases	MGC40053, GASP4
Ensembl gene	ENSG00000196440
Ensembl biotype	protein_coding
OMIM	301046
Entrez	100131755

Gene structure

Transcript identifiers

Ensembl transcripts: 10 — 5 protein_coding_CDS_not_defined, 4 nonsense_mediated_decay, 1 protein_coding

ENST00000354842, ENST00000423738, ENST00000430461, ENST00000431677, ENST00000433011, ENST00000442270, ENST00000445416, ENST00000452188, ENST00000453574, ENST00000455331

RefSeq mRNA: 1 — MANE Select: NM_001256155 NM_001256155

CCDS: CCDS59170

Canonical transcript exons

ENST00000423738 — 6 exons

Exon	Start	End
ENSE00001678603	101485456	101485530
ENSE00001772449	101488444	101495807
ENSE00002215802	101486023	101486092
ENSE00002218889	101487193	101487272
ENSE00002284439	101487608	101487691
ENSE00003583780	101488044	101488099

Expression profiles

Bgee: expression breadth ubiquitous, 239 present calls, max score 92.46.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 10.8120 / max 330.1331, expressed in 1427 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter ID	TPM avg	Samples expressed
196962	8.4095	1206
196961	1.7121	805
196960	0.5122	247
209759	0.1782	79

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
left ovary	UBERON:0002119	92.46	gold quality
type B pancreatic cell	CL:0000169	92.13	gold quality
right ovary	UBERON:0002118	91.19	gold quality
adenohypophysis	UBERON:0002196	91.08	gold quality
left lobe of thyroid gland	UBERON:0001120	90.35	gold quality
pituitary gland	UBERON:0000007	90.18	gold quality
right lobe of thyroid gland	UBERON:0001119	89.92	gold quality
thyroid gland	UBERON:0002046	89.47	gold quality
olfactory bulb	UBERON:0002264	89.25	gold quality
body of uterus	UBERON:0009853	89.14	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	89.01	gold quality
muscle layer of sigmoid colon	UBERON:0035805	88.92	gold quality
ovary	UBERON:0000992	88.59	gold quality
lower esophagus muscularis layer	UBERON:0035833	88.25	gold quality
lower esophagus	UBERON:0013473	88.19	gold quality
mucosa of stomach	UBERON:0001199	88.12	gold quality
left adrenal gland cortex	UBERON:0035825	88.03	gold quality
sural nerve	UBERON:0015488	87.93	gold quality
right hemisphere of cerebellum	UBERON:0014890	87.81	gold quality
right uterine tube	UBERON:0001302	87.50	gold quality
tibial nerve	UBERON:0001323	87.50	gold quality
right adrenal gland cortex	UBERON:0035827	87.39	gold quality
left uterine tube	UBERON:0001303	87.38	gold quality
cerebellar hemisphere	UBERON:0002245	87.13	gold quality
calcaneal tendon	UBERON:0003701	87.12	gold quality
left adrenal gland	UBERON:0001234	87.06	gold quality
cerebellar cortex	UBERON:0002129	86.97	gold quality
popliteal artery	UBERON:0002250	86.93	gold quality
tibial artery	UBERON:0007610	86.90	gold quality
right adrenal gland	UBERON:0001233	86.77	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	5.81

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

28 targeting ARMCX4, 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-8485	100.00	77.57	4731
HSA-MIR-6740-5P	100.00	65.64	932
HSA-MIR-450A-1-3P	100.00	69.33	1837
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-3185	99.99	68.12	1959
HSA-MIR-568	99.98	69.86	2084
HSA-MIR-607	99.97	73.62	5593
HSA-MIR-4267	99.96	66.53	2368
HSA-MIR-4760-3P	99.93	70.50	2385
HSA-MIR-579-3P	99.86	71.66	3628
HSA-MIR-664B-3P	99.84	71.65	3590
HSA-MIR-577	99.78	69.13	2479
HSA-MIR-5700	99.64	69.88	2280
HSA-MIR-4328	99.57	71.06	4094
HSA-MIR-4452	99.50	68.45	1493
HSA-MIR-12132	99.47	68.90	1341
HSA-MIR-372-5P	99.41	69.11	2299
HSA-MIR-888-5P	99.30	70.15	1855
HSA-MIR-10522-5P	99.26	68.50	2087
HSA-MIR-6071	99.16	67.77	1780
HSA-MIR-8060	98.61	66.93	1187
HSA-MIR-767-3P	98.61	67.69	1192
HSA-MIR-6502-3P	97.86	65.43	569
HSA-MIR-4724-3P	97.57	67.31	785
HSA-MIR-6847-3P	96.50	67.30	582
HSA-MIR-549A-5P	96.35	68.08	587
HSA-MIR-6828-3P	96.06	67.61	1155
HSA-MIR-6816-3P	95.05	66.08	459

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	armc10	ENSDARG00000062960
mus_musculus	Armcx4	ENSMUSG00000049804
rattus_norvegicus	Armcx4	ENSRNOG00000043128
caenorhabditis_elegans		WBGENE00013456

Paralogs (10): ARMCX3 (ENSG00000102401), ARMCX5 (ENSG00000125962), ARMCX1 (ENSG00000126947), ARMC12 (ENSG00000157343), GPRASP2 (ENSG00000158301), ARMC10 (ENSG00000170632), ARMCX2 (ENSG00000184867), GPRASP3 (ENSG00000198908), GPRASP1 (ENSG00000198932), ARMCX6 (ENSG00000198960)

Protein

Protein identifiers

Armadillo repeat-containing X-linked protein 4 — Q5H9R4 (reviewed: Q5H9R4)

All UniProt accessions (2): A0A8J9A6E2, Q5H9R4

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Membrane.

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

Isoforms (3)

UniProt ID	Names	Canonical?
Q5H9R4-1	1	yes
Q5H9R4-2	2
Q5H9R4-3	3

RefSeq proteins (1): NP_001243084* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR000225	Armadillo	Repeat
IPR006911	ARM-rpt_dom	Domain
IPR011989	ARM-like	Homologous_superfamily
IPR016024	ARM-type_fold	Homologous_superfamily

Pfam: PF04826

UniProt features (33 total): compositionally biased region 11, region of interest 8, repeat 4, splice variant 4, sequence conflict 3, chain 1, transmembrane region 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q5H9R4-F1	40.98	0.02

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 117 (showing top): GSE45365_CD8A_DC_VS_CD11B_DC_IFNAR_KO_MCMV_INFECTION_DN, GGGTGGRR_PAX4_03, TGACATY_UNKNOWN, TURASHVILI_BREAST_DUCTAL_CARCINOMA_VS_DUCTAL_NORMAL_DN, RYTTCCTG_ETS2_B, OCT1_B, IVANOVA_HEMATOPOIESIS_EARLY_PROGENITOR, TGGAAA_NFAT_Q4_01, GAVIN_FOXP3_TARGETS_CLUSTER_P3, GAVIN_IL2_RESPONSIVE_FOXP3_TARGETS_UP, YKACATTT_UNKNOWN, CDC5_01, LIU_PROSTATE_CANCER_DN, GARGALOVIC_RESPONSE_TO_OXIDIZED_PHOSPHOLIPIDS_TURQUOISE_DN, WONG_ADULT_TISSUE_STEM_MODULE

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

982 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ARMCX4	MFSD6L	Q8IWD5	560
ARMCX4	SH3RF2	Q8TEC5	508
ARMCX4	ZNF605	Q86T29	507
ARMCX4	CACHD1	Q5VU97	503
ARMCX4	NECAB3	Q96P71	498
ARMCX4	TRAPPC12	Q8WVT3	493
ARMCX4	AP4S1	Q9Y587	483
ARMCX4	ZSCAN29	Q8IWY8	480
ARMCX4	UBAC2	Q8NBM4	475
ARMCX4	CCDC163	A0A0D9SF12	474
ARMCX4	RHPN1	Q8TCX5	463
ARMCX4	TAX1BP3	O14907	460
ARMCX4	RAB30	Q15771	457
ARMCX4	S100A5	P33763	456
ARMCX4	DPAGT1	Q9H3H5	441

IntAct

4 interactions, top by confidence:

A	B	Type	Score
ARMCX4	PRKACB	psi-mi:“MI:0914”(association)	0.350
KLHL22	TRAV18	psi-mi:“MI:0914”(association)	0.350
HUNK	ARMCX4	psi-mi:“MI:0915”(physical association)	0.000

ESM2 similar proteins: A0A0J9YWL9, A0A0J9YY54, A0A0U1RQI7, A0A494C071, A6NNC1, A6QL64, B3KS81, D3YZV8, E2RYF7, E9Q6E9, F1LWT0, F8W0I5, O60732, P0C8Z4, P0DKJ7, P0DKJ8, P0DKL2, P0DPF3, P18751, P20930, P43537, P53353, P59797, P62521, Q01456, Q08AG5, Q12816, Q3BBV2, Q5H9R4, Q5HY64, Q5JPF3, Q6P902, Q6ZQX7, Q86T75, Q86VE3, Q86VQ3, Q8BGJ3, Q8N307, Q8N7U7, Q8N7X1

Diamond homologs: B1WBW4, Q3UZB0, Q5H9R4, Q5JY77, Q5R4B2, Q5R7U0, Q5R9J3, Q5RDG2, Q5U310, Q5U4C1, Q5XID7, Q6A058, Q6P1M9, Q6PI77, Q7L311, Q8BHS6, Q8BUY8, Q8N2F6, Q920R4, Q96D09, Q9BE11, Q9CX83, Q9D0L7, Q9P291, Q9UH62, Q6PB60, Q71HP2, Q7L4S7, Q66HF0, Q8K3A6

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

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

Top pathogenic / likely-pathogenic (0)

SpliceAI

165 predictions. Top by Δscore:

Variant	Effect	Δscore
X:101488098:AGGT:A	donor_loss	0.9900
X:101488098:AGGTT:A	donor_gain	0.9700
X:101488100:G:GG	donor_gain	0.9200
X:101488097:CAGGT:C	donor_gain	0.9000
X:101488099:GGTT:G	donor_gain	0.8600
X:101489312:GACT:G	donor_gain	0.8600
X:101488096:ACAGG:A	donor_gain	0.8500
X:101488504:GCC:G	donor_gain	0.8500
X:101488100:G:A	donor_gain	0.8400
X:101489316:G:GG	donor_gain	0.8400
X:101488101:T:A	donor_gain	0.8000
X:101489307:G:GT	donor_gain	0.7900
X:101488095:TACAG:T	donor_gain	0.7800
X:101489461:A:AG	donor_gain	0.7400
X:101488074:G:GT	donor_gain	0.7100
X:101488070:A:T	donor_gain	0.7000
X:101488586:T:G	donor_gain	0.6800
X:101488605:G:GT	donor_gain	0.6600
X:101488438:TTCTA:T	acceptor_loss	0.6400
X:101488439:TCTAG:T	acceptor_loss	0.6400
X:101488440:CTAGG:C	acceptor_loss	0.6400
X:101488441:TA:T	acceptor_loss	0.6400
X:101488442:AGGT:A	acceptor_loss	0.6400
X:101488443:GGTCC:G	acceptor_loss	0.6400
X:101489325:GC:G	donor_gain	0.6400
X:101488436:A:AG	acceptor_loss	0.6200
X:101489315:T:TG	donor_gain	0.6000
X:101488585:A:AG	donor_gain	0.5300
X:101489326:C:G	donor_gain	0.5000
X:101492077:T:G	donor_gain	0.4900

AlphaMissense

15029 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
X:101495149:T:C	L2187P	0.998
X:101495389:T:C	L2267P	0.998
X:101495023:T:C	L2145P	0.997
X:101495262:G:C	A2225P	0.997
X:101495266:T:C	L2226P	0.997
X:101495272:T:C	L2228P	0.997
X:101494774:C:A	A2062D	0.996
X:101494909:T:C	L2107P	0.996
X:101495041:T:C	L2151P	0.996
X:101495095:T:C	L2169P	0.996
X:101495191:T:C	L2201P	0.996
X:101494726:T:C	L2046P	0.995
X:101495215:T:C	L2209P	0.995
X:101495227:T:C	F2213S	0.995
X:101495263:C:A	A2225D	0.995
X:101495389:T:A	L2267H	0.995
X:101495071:T:A	V2161D	0.994
X:101495149:T:G	L2187R	0.994
X:101495188:T:C	L2200S	0.994
X:101494773:G:C	A2062P	0.993
X:101494896:G:C	A2103P	0.993
X:101495158:T:C	F2190S	0.993
X:101495196:G:C	A2203P	0.993
X:101495437:T:A	V2283D	0.993
X:101494905:G:C	A2106P	0.992
X:101495137:T:A	V2183D	0.992
X:101495149:T:A	L2187H	0.992
X:101495161:C:T	S2191F	0.992
X:101495331:T:C	F2248L	0.992
X:101495333:C:A	F2248L	0.992

dbSNP variants (sampled 300 via entrez): RS1000015794 (X:101457275 A>C,G), RS1000066532 (X:101456635 A>T), RS1000176047 (X:101466594 A>G), RS1000264757 (X:101448090 C>A,T), RS1000293495 (X:101479960 T>A,C), RS1000364523 (X:101528278 C>G), RS1000434120 (X:101420290 C>T), RS1000445968 (X:101489629 T>C), RS1000473082 (X:101527165 A>G), RS1000528302 (X:101466916 A>G), RS1000777168 (X:101417800 C>A,T), RS1000816227 (X:101487057 G>C), RS1000887370 (X:101499348 G>A), RS1000911556 (X:101464604 C>T), RS1000991328 (X:101427381 C>T)

Disease associations

OMIM: gene MIM:301046 | 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

24 total (human), top 24 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects cotreatment, decreases expression	4
Benzo(a)pyrene	affects methylation, decreases expression	3
Nickel	decreases expression	2
Smoke	decreases expression, increases expression	2
Cadmium Chloride	increases abundance, increases expression	2
GSK-J4	decreases expression	1
FR900359	increases phosphorylation	1
triphenyl phosphate	affects expression	1
sodium arsenite	decreases expression	1
nickel sulfate	decreases expression	1
di-n-butylphosphoric acid	affects expression	1
entinostat	decreases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, decreases expression	1
abrine	increases expression	1
dorsomorphin	affects cotreatment, decreases expression	1
(+)-JQ1 compound	decreases expression	1
Vorinostat	affects cotreatment, decreases expression	1
Cadmium	increases abundance, increases expression	1
Endosulfan	increases expression	1
Thiram	increases expression	1
Tobacco Smoke Pollution	decreases expression	1
8-Bromo Cyclic Adenosine Monophosphate	increases expression	1
Aflatoxin B1	affects methylation	1
Antirheumatic Agents	increases expression	1

Clinical trials (associated diseases)

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