ARMCX5

Summary

ARMCX5 (armadillo repeat containing X-linked 5, HGNC:25772) is a protein-coding gene on chromosome Xq22.1, encoding Armadillo repeat-containing X-linked protein 5 (Q6P1M9).

At a glance

• Clinical variants (ClinVar): 62 total — 1 pathogenic
• MANE Select transcript: NM_001168478

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:25772
Approved symbol	ARMCX5
Name	armadillo repeat containing X-linked 5
Location	Xq22.1
Locus type	gene with protein product
Status	Approved
Aliases	FLJ12969, GASP5
Ensembl gene	ENSG00000125962
Ensembl biotype	protein_coding
OMIM	301047
Entrez	64860

Gene structure

Transcript identifiers

Ensembl transcripts: 17 — 17 protein_coding

ENST00000246174, ENST00000372742, ENST00000473968, ENST00000477663, ENST00000479502, ENST00000604957, ENST00000859969, ENST00000859970, ENST00000859971, ENST00000859972, ENST00000859973, ENST00000859974, ENST00000859975, ENST00000859976, ENST00000947902, ENST00000947903, ENST00000947904

RefSeq mRNA: 6 — MANE Select: NM_001168478 NM_001168478, NM_001168479, NM_001168480, NM_001168482, NM_001168485, NM_022838

CCDS: CCDS14500

Canonical transcript exons

ENST00000473968 — 4 exons

Exon	Start	End
ENSE00001458523	102601880	102604159
ENSE00001933766	102599515	102599847
ENSE00003695138	102600920	102601032
ENSE00003699751	102601464	102601509

Expression profiles

Bgee: expression breadth ubiquitous, 267 present calls, max score 87.02.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.3455 / max 11.9754, expressed in 179 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
196984	15.8375	1738
196983	0.3455	179

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
islet of Langerhans	UBERON:0000006	87.02	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	85.07	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	83.40	gold quality
pancreas	UBERON:0001264	83.05	gold quality
hair follicle	UBERON:0002073	82.69	silver quality
epithelium of nasopharynx	UBERON:0001951	82.50	gold quality
nasopharynx	UBERON:0001728	82.49	gold quality
corpus epididymis	UBERON:0004359	81.64	gold quality
body of pancreas	UBERON:0001150	81.59	gold quality
rectum	UBERON:0001052	81.46	gold quality
cartilage tissue	UBERON:0002418	81.38	gold quality
cortical plate	UBERON:0005343	80.94	gold quality
mucosa of paranasal sinus	UBERON:0005030	80.33	gold quality
mucosa of sigmoid colon	UBERON:0004993	79.85	gold quality
nasal cavity mucosa	UBERON:0001826	79.79	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	79.79	gold quality
calcaneal tendon	UBERON:0003701	79.61	gold quality
monocyte	CL:0000576	79.37	gold quality
adrenal tissue	UBERON:0018303	79.34	gold quality
stromal cell of endometrium	CL:0002255	79.30	gold quality
mononuclear cell	CL:0000842	79.27	gold quality
leukocyte	CL:0000738	79.18	gold quality
caput epididymis	UBERON:0004358	79.06	gold quality
colonic mucosa	UBERON:0000317	78.91	gold quality
esophagus squamous epithelium	UBERON:0006920	78.74	gold quality
prefrontal cortex	UBERON:0000451	78.72	gold quality
left adrenal gland	UBERON:0001234	78.48	gold quality
left adrenal gland cortex	UBERON:0035825	78.40	gold quality
descending thoracic aorta	UBERON:0002345	78.33	gold quality
prostate gland	UBERON:0002367	78.19	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	3.05

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

36 targeting ARMCX5, 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-4789-3P	99.99	70.75	2484
HSA-MIR-196A-1-3P	99.99	72.15	2772
HSA-MIR-371B-5P	99.99	75.34	4759
HSA-MIR-186-5P	99.99	70.83	3707
HSA-MIR-373-5P	99.98	75.36	4753
HSA-MIR-616-5P	99.98	75.58	4775
HSA-MIR-3148	99.97	75.06	6478
HSA-MIR-6778-3P	99.96	67.29	2693
HSA-MIR-6835-3P	99.93	70.49	2904
HSA-MIR-374A-5P	99.90	71.34	2923
HSA-MIR-6124	99.87	69.78	3551
HSA-MIR-4802-3P	99.72	70.13	1273
HSA-MIR-4422	99.72	72.07	2908
HSA-MIR-29B-2-5P	99.67	68.98	1726
HSA-MIR-466	99.67	70.85	2863
HSA-MIR-586	99.65	70.40	2051
HSA-MIR-891B	99.59	69.81	1083
HSA-MIR-216A-5P	99.50	68.02	1288
HSA-MIR-513C-5P	99.50	68.42	1730
HSA-MIR-514B-5P	99.50	68.19	1766
HSA-MIR-548G-3P	99.48	68.67	2159
HSA-MIR-519D-5P	99.41	69.30	2057
HSA-MIR-1304-5P	98.90	68.58	1054
HSA-MIR-11399	98.71	65.69	869
HSA-MIR-3188	98.58	65.60	878
HSA-MIR-3145-5P	98.57	67.83	900
HSA-MIR-5585-3P	98.25	67.41	941
HSA-MIR-3664-3P	97.85	67.62	1452
HSA-MIR-1279	97.83	67.50	1898
HSA-MIR-376A-5P	97.70	65.61	863

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	armc10	ENSDARG00000062960
mus_musculus	Armcx5	ENSMUSG00000072969
rattus_norvegicus	Armcx5	ENSRNOG00000003187
caenorhabditis_elegans		WBGENE00013456

Paralogs (10): ARMCX3 (ENSG00000102401), ARMCX1 (ENSG00000126947), ARMC12 (ENSG00000157343), GPRASP2 (ENSG00000158301), ARMC10 (ENSG00000170632), ARMCX2 (ENSG00000184867), ARMCX4 (ENSG00000196440), GPRASP3 (ENSG00000198908), GPRASP1 (ENSG00000198932), ARMCX6 (ENSG00000198960)

Protein

Protein identifiers

Armadillo repeat-containing X-linked protein 5 — Q6P1M9 (reviewed: Q6P1M9)

All UniProt accessions (4): Q6P1M9, A0A0G2JLJ9, S4R3L0, S4R3L5

UniProt curated annotations — full annotation on UniProt →

Similarity. Belongs to the eutherian X-chromosome-specific Armcx family.

RefSeq proteins (6): NP_001161950, NP_001161951, NP_001161952, NP_001161954, NP_001161957, NP_073749 (=MANE)

Domains & families (InterPro)

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

Pfam: PF04826

UniProt features (12 total): repeat 4, region of interest 3, sequence conflict 2, compositionally biased region 2, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q6P1M9-F1	54.59	0.14

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 73 (showing top): GSE18804_SPLEEN_MACROPHAGE_VS_BRAIN_TUMORAL_MACROPHAGE_UP, GSE37336_LY6C_POS_VS_NEG_NAIVE_CD4_TCELL_UP, GSE18804_SPLEEN_MACROPHAGE_VS_TUMORAL_MACROPHAGE_UP, GSE18804_BRAIN_VS_COLON_TUMORAL_MACROPHAGE_UP, SHEDDEN_LUNG_CANCER_GOOD_SURVIVAL_A5, MODULE_48, MODULE_207, MODULE_95, BENPORATH_OCT4_TARGETS, chrXq22, WIERENGA_STAT5A_TARGETS_DN, MODULE_163, ERBB2_UP.V1_DN, LTE2_UP.V1_DN, MEK_UP.V1_DN

GO Biological Process (0):

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

GO Cellular Component (0):

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
binding	1

Protein interactions and networks

STRING

901 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ARMCX5	UBLCP1	Q8WVY7	531
ARMCX5	ZNF543	Q08ER8	480
ARMCX5	VOPP1	Q96AW1	464
ARMCX5	OR4K2	Q8NGD2	431
ARMCX5	GPR174	Q9BXC1	372
ARMCX5	ANKDD1A	Q495B1	351
ARMCX5	URM1	Q9BTM9	343
ARMCX5	A8MYK1	A8MYK1	323
ARMCX5	ZNF518B	Q9C0D4	322
ARMCX5	YIPF6	Q96EC8	317
ARMCX5	ARMCX6	Q7L4S7	316
ARMCX5	PLEKHO2	Q8TD55	313
ARMCX5	NXF3	Q9H4D5	311
ARMCX5	GPRASP2	Q96D09	310
ARMCX5	DHX35	Q9H5Z1	309

IntAct

40 interactions, top by confidence:

A	B	Type	Score
APPBP2	ARMCX5	psi-mi:“MI:0915”(physical association)	0.720
ARMCX5	APPBP2	psi-mi:“MI:0915”(physical association)	0.720
HTT	ARMCX5	psi-mi:“MI:0915”(physical association)	0.560
ALOX5	DDHD2	psi-mi:“MI:0914”(association)	0.530
ZNRD2	MYO9A	psi-mi:“MI:0914”(association)	0.530
CAMK2D	ELP1	psi-mi:“MI:0914”(association)	0.530
ZNRD2	CCDC85C	psi-mi:“MI:0914”(association)	0.530
ARMCX5	CANX	psi-mi:“MI:0915”(physical association)	0.400
MAPK6		psi-mi:“MI:0914”(association)	0.350
RIPK4	VWA8	psi-mi:“MI:0914”(association)	0.350
M		psi-mi:“MI:0914”(association)	0.350
FKBP5	IFT56	psi-mi:“MI:0914”(association)	0.350
FKBP8	GNB5	psi-mi:“MI:0914”(association)	0.350
PTGES3	KIFBP	psi-mi:“MI:0914”(association)	0.350
PTGES3	SBNO1	psi-mi:“MI:0914”(association)	0.350
TNFRSF1B	MAP3K7	psi-mi:“MI:0914”(association)	0.350
FTL	SH3PXD2B	psi-mi:“MI:0914”(association)	0.350
INF2	PIPSL	psi-mi:“MI:0914”(association)	0.350
EEF1AKMT3	SMCHD1	psi-mi:“MI:0914”(association)	0.350
UBXN6	ZSWIM8	psi-mi:“MI:0914”(association)	0.350
SULT1C4	ZSWIM8	psi-mi:“MI:0914”(association)	0.350
CRYBB3	ARHGAP32	psi-mi:“MI:0914”(association)	0.350

BioGRID (48): ARMCX5 (Two-hybrid), ARMCX5 (Synthetic Growth Defect), ARMCX5 (Affinity Capture-MS), ARMCX5 (Affinity Capture-MS), ARMCX5 (Affinity Capture-MS), ARMCX5 (Affinity Capture-MS), ARMCX5 (Affinity Capture-MS), ARMCX5 (Two-hybrid), ARMCX5 (Proximity Label-MS), ARMCX5 (Proximity Label-MS), ARMCX5 (Affinity Capture-RNA), ARMCX5 (Affinity Capture-MS), ARMCX5 (Affinity Capture-MS), ARMCX5 (Affinity Capture-MS), ARMCX5 (Affinity Capture-MS)

ESM2 similar proteins: A0A1B0GVN3, A1KXM5, A2AEY4, A6NFE2, A6QQS3, A7A061, A7KBS4, A8MTZ7, B3LRH6, B4HGK2, B4QT24, B5VMP2, E1JH25, F4KIH4, F6XZJ7, O36020, O49498, O74981, O94713, O96001, P21691, P22575, P88825, Q11194, Q2YDJ5, Q32MG2, Q3URS2, Q4V8E9, Q5BB76, Q5JRM2, Q5R7U0, Q5RDG2, Q6AXV6, Q6AXY9, Q6P1M9, Q6PI77, Q80VJ6, Q810T2, Q8BUY8, Q8NA61

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

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

Classification	Count (floor)
Pathogenic	1
Likely pathogenic	0
Uncertain significance	58
Likely benign	2
Benign	0

Top pathogenic / likely-pathogenic (1)

Variant ID	HGVS	Classification
1526833	GRCh37/hg19 Xq22.1-22.2(chrX:101331999-102771372)	Pathogenic

SpliceAI

731 predictions. Top by Δscore:

Variant	Effect	Δscore
X:102599259:A:T	donor_gain	0.9900
X:102599812:GAAA:G	donor_gain	0.9900
X:102599258:G:GT	donor_gain	0.9800
X:102599625:G:GT	donor_gain	0.9800
X:102599843:AGAAG:A	donor_loss	0.9800
X:102599844:GAAG:G	donor_gain	0.9800
X:102599844:GAAGG:G	donor_loss	0.9800
X:102599845:AAGGT:A	donor_loss	0.9800
X:102599846:AGGT:A	donor_loss	0.9800
X:102599847:GGTC:G	donor_loss	0.9800
X:102599848:G:A	donor_loss	0.9800
X:102599849:T:A	donor_loss	0.9800
X:102599808:C:T	donor_gain	0.9700
X:102599851:A:AG	donor_gain	0.9700
X:102599852:G:GG	donor_gain	0.9700
X:102601874:CCCTA:C	acceptor_loss	0.9600
X:102601875:CCTA:C	acceptor_loss	0.9600
X:102601877:TAG:T	acceptor_loss	0.9600
X:102601878:AGGTC:A	acceptor_loss	0.9600
X:102601458:CCATA:C	acceptor_loss	0.9500
X:102601459:CATA:C	acceptor_loss	0.9500
X:102601461:TAGGT:T	acceptor_loss	0.9500
X:102601462:A:C	acceptor_loss	0.9500
X:102601463:G:GA	acceptor_loss	0.9500
X:102601506:CAAGG:C	donor_loss	0.9500
X:102601508:AGGT:A	donor_loss	0.9500
X:102601509:GG:G	donor_loss	0.9500
X:102599262:GAATG:G	donor_gain	0.9400
X:102601455:T:A	acceptor_loss	0.9400
X:102601512:A:AG	donor_loss	0.9400

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000107889 (X:102600998 T>A), RS1000634112 (X:102603207 A>G), RS1000666618 (X:102602551 A>T), RS1000714514 (X:102603990 G>A), RS1001230523 (X:102604500 A>G), RS1001556791 (X:102604621 G>A), RS1002086684 (X:102601669 C>A,G,T), RS1003530922 (X:102599595 G>T), RS1003562121 (X:102599779 C>G,T), RS1005203863 (X:102601608 C>T), RS1005233146 (X:102600891 T>C), RS1005274566 (X:102603916 A>G), RS1007671313 (X:102600807 G>C), RS1007700710 (X:102600341 T>G), RS1008001640 (X:102599059 C>T)

Disease associations

OMIM: gene MIM:301047 | 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

29 total (human), top 29 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	increases methylation, affects expression, decreases expression	3
Cyclosporine	increases expression	2
dicrotophos	decreases expression	1
bisphenol A	decreases methylation	1
sodium arsenite	affects cotreatment, increases abundance, increases expression	1
manganese chloride	increases abundance, increases expression, affects cotreatment	1
potassium chromate(VI)	decreases expression	1
di-n-butylphosphoric acid	affects expression	1
CGP 52608	affects binding, increases reaction	1
abrine	increases expression	1
2-methyl-2H-pyrazole-3-carboxylic acid (2-methyl-4-o-tolylazophenyl)amide	decreases expression, decreases reaction	1
NSC 689534	affects binding, increases expression	1
Acetaminophen	decreases expression	1
Air Pollutants	decreases expression, increases abundance	1
Arsenic	affects cotreatment, increases abundance, increases expression	1
Vehicle Emissions	decreases expression, decreases reaction	1
Benzo(a)pyrene	affects methylation	1
Copper	affects binding, increases expression	1
Doxorubicin	decreases expression	1
Manganese	increases abundance, increases expression, affects cotreatment	1
Quercetin	decreases expression	1
Smoke	decreases expression, increases abundance	1
Thimerosal	increases expression	1
Urethane	decreases expression	1
Aflatoxin B1	decreases methylation	1
Sodium Selenite	increases expression	1
Antirheumatic Agents	increases expression	1
Acrylamide	decreases expression	1
Particulate Matter	decreases expression, decreases reaction	1

Clinical trials (associated diseases)

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