ARMCX6

Summary

ARMCX6 (armadillo repeat containing X-linked 6, HGNC:26094) is a protein-coding gene on chromosome Xq22.1, encoding Protein ARMCX6 (Q7L4S7). May regulate the dynamics and distribution of mitochondria in neural cells.

Predicted to be located in mitochondrial outer membrane. Predicted to be active in mitochondrion.

Source: NCBI Gene 54470 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 36 total — 1 pathogenic
• MANE Select transcript: NM_019007

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:26094
Approved symbol	ARMCX6
Name	armadillo repeat containing X-linked 6
Location	Xq22.1
Locus type	gene with protein product
Status	Approved
Aliases	FLJ20811, GASP10
Ensembl gene	ENSG00000198960
Ensembl biotype	protein_coding
OMIM	301048
Entrez	54470

Gene structure

Transcript identifiers

Ensembl transcripts: 17 — 12 protein_coding, 5 protein_coding_CDS_not_defined

ENST00000361910, ENST00000462302, ENST00000467089, ENST00000494624, ENST00000495964, ENST00000497931, ENST00000538627, ENST00000539247, ENST00000854158, ENST00000854159, ENST00000854160, ENST00000922607, ENST00000922608, ENST00000922609, ENST00000922610, ENST00000922611, ENST00000953411

RefSeq mRNA: 3 — MANE Select: NM_019007 NM_001009584, NM_001184768, NM_019007

CCDS: CCDS14488

Canonical transcript exons

ENST00000361910 — 3 exons

Exon	Start	End
ENSE00001032424	101617503	101617584
ENSE00001820534	101615125	101616766
ENSE00001915848	101617885	101618000

Expression profiles

Bgee: expression breadth ubiquitous, 134 present calls, max score 94.77.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 39.0992 / max 595.3434, expressed in 1804 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
199960	39.0992	1804

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
adrenal tissue	UBERON:0018303	94.77	gold quality
right adrenal gland cortex	UBERON:0035827	94.71	gold quality
right adrenal gland	UBERON:0001233	94.51	gold quality
body of pancreas	UBERON:0001150	93.91	gold quality
left adrenal gland cortex	UBERON:0035825	93.37	gold quality
smooth muscle tissue	UBERON:0001135	93.34	gold quality
left adrenal gland	UBERON:0001234	93.32	gold quality
pancreas	UBERON:0001264	93.31	gold quality
islet of Langerhans	UBERON:0000006	93.16	gold quality
stromal cell of endometrium	CL:0002255	93.00	gold quality
adrenal gland	UBERON:0002369	92.93	gold quality
spleen	UBERON:0002106	92.75	gold quality
monocyte	CL:0000576	92.44	gold quality
leukocyte	CL:0000738	92.26	gold quality
right coronary artery	UBERON:0001625	92.23	gold quality
lymph node	UBERON:0000029	91.98	gold quality
popliteal artery	UBERON:0002250	91.81	gold quality
tibial artery	UBERON:0007610	91.81	gold quality
granulocyte	CL:0000094	91.64	gold quality
descending thoracic aorta	UBERON:0002345	91.50	gold quality
cortical plate	UBERON:0005343	91.48	gold quality
apex of heart	UBERON:0002098	91.47	gold quality
tonsil	UBERON:0002372	91.45	gold quality
cortex of kidney	UBERON:0001225	91.26	gold quality
saliva-secreting gland	UBERON:0001044	91.13	gold quality
pituitary gland	UBERON:0000007	91.08	gold quality
adenohypophysis	UBERON:0002196	91.07	gold quality
placenta	UBERON:0001987	91.05	gold quality
gall bladder	UBERON:0002110	91.05	gold quality
ganglionic eminence	UBERON:0004023	91.01	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	4.18
E-CURD-112	no	3.03

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

28 targeting ARMCX6, 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-6077	99.99	68.04	2299
HSA-MIR-1321	99.84	65.30	1811
HSA-MIR-4739	99.84	65.25	1832
HSA-MIR-4756-5P	99.84	64.98	1809
HSA-MIR-6756-5P	99.82	67.97	2466
HSA-MIR-6745	99.74	65.33	1321
HSA-MIR-6766-5P	99.68	67.70	2325
HSA-MIR-3158-5P	99.65	67.51	1763
HSA-MIR-6134	99.63	65.68	1537
HSA-MIR-105-5P	99.54	69.24	2060
HSA-MIR-7853-5P	99.54	69.30	2055
HSA-MIR-7106-5P	99.53	67.47	3574
HSA-MIR-363-5P	99.46	64.51	1015
HSA-MIR-330-3P	99.41	69.95	2521
HSA-MIR-1276	99.36	68.18	1642
HSA-MIR-4727-5P	99.23	67.55	1154
HSA-MIR-661	99.09	65.94	2062
HSA-MIR-6738-3P	99.03	67.14	1326
HSA-MIR-2276-3P	98.76	67.75	1384
HSA-MIR-655-5P	98.74	65.93	888
HSA-MIR-1537-5P	98.70	68.33	999
HSA-MIR-4483	98.09	64.12	1642
HSA-MIR-4772-3P	98.04	65.60	1203
HSA-MIR-3116	97.07	65.78	1324
HSA-MIR-6894-3P	96.73	65.64	798
HSA-MIR-4714-3P	96.53	67.44	452
HSA-MIR-1293	96.16	64.69	916
HSA-MIR-4754	88.00	62.03	37

Literature-anchored findings (GeneRIF, showing 1)

• An X Chromosome Transcriptome Wide Association Study Implicates ARMCX6 in Alzheimer’s Disease. (PMID:38489177)

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	armc10	ENSDARG00000062960
mus_musculus	Armcx6	ENSMUSG00000050394
rattus_norvegicus	Armcx6	ENSRNOG00000037707
caenorhabditis_elegans		WBGENE00013456

Paralogs (10): ARMCX3 (ENSG00000102401), ARMCX5 (ENSG00000125962), ARMCX1 (ENSG00000126947), ARMC12 (ENSG00000157343), GPRASP2 (ENSG00000158301), ARMC10 (ENSG00000170632), ARMCX2 (ENSG00000184867), ARMCX4 (ENSG00000196440), GPRASP3 (ENSG00000198908), GPRASP1 (ENSG00000198932)

Protein

Protein identifiers

Protein ARMCX6 — Q7L4S7 (reviewed: Q7L4S7)

All UniProt accessions (1): Q7L4S7

UniProt curated annotations — full annotation on UniProt →

Function. May regulate the dynamics and distribution of mitochondria in neural cells.

Subcellular location. Mitochondrion. Mitochondrion outer membrane.

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

RefSeq proteins (3): NP_001009584, NP_001171697, NP_061880* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR006911	ARM-rpt_dom	Domain
IPR051303	Armcx_regulator	Family

Pfam: PF04826

UniProt features (8 total): region of interest 4, topological domain 2, chain 1, transmembrane region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q7L4S7-F1	44.47	0.00

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 118 (showing top): GOBP_AXO_DENDRITIC_TRANSPORT, GAANYNYGACNY_UNKNOWN, MEF2_02, GOBP_ORGANELLE_TRANSPORT_ALONG_MICROTUBULE, IRF7_01, CCANNAGRKGGC_UNKNOWN, USF_01, WTGAAAT_UNKNOWN, E4F1_Q6, SCHAEFFER_PROSTATE_DEVELOPMENT_48HR_DN, GOCC_MITOCHONDRIAL_ENVELOPE, ZHOU_INFLAMMATORY_RESPONSE_LIVE_DN, IRF_Q6, USF_02, GOCC_NEURON_PROJECTION

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (3): mitochondrion (GO:0005739), mitochondrial outer membrane (GO:0005741), membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cytoplasm	1
intracellular membrane-bounded organelle	1
mitochondrial membrane	1
organelle outer membrane	1
cellular anatomical structure	1

Protein interactions and networks

STRING

344 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ARMCX6	C10orf62	Q5T681	574
ARMCX6	CFAP141	Q5VU69	507
ARMCX6	OR5M3	Q8NGP4	475
ARMCX6	ZNF285	Q96NJ3	447
ARMCX6	XAGE5	Q8WWM1	419
ARMCX6	DRG1	Q9Y295	415
ARMCX6	PASK	Q96RG2	411
ARMCX6	TRAPPC6B	Q86SZ2	389
ARMCX6	NIBAN3	Q86XR2	389
ARMCX6	GRPEL2	Q8TAA5	380
ARMCX6	ZNF277	Q9NRM2	376
ARMCX6	TRAK2	O60296	366
ARMCX6	SLC12A9	Q9BXP2	360
ARMCX6	CRACD	Q6ZU35	346
ARMCX6	XKR6	Q5GH73	323

IntAct

2 interactions, top by confidence:

A	B	Type	Score
ARMCX6	TNPO2	psi-mi:“MI:0914”(association)	0.350

BioGRID (8): ARMCX6 (Affinity Capture-RNA), ARMCX6 (Affinity Capture-RNA), ARMCX6 (Positive Genetic), TUBB2B (Affinity Capture-MS), TNPO1 (Affinity Capture-MS), MYD88 (Affinity Capture-MS), TNPO2 (Affinity Capture-MS), ARMCX6 (Affinity Capture-RNA)

ESM2 similar proteins: A0A1B0GTK4, A0JNL8, A2RU37, A4D1N5, B1A0U8, B1ANY3, F2Z398, G3V211, J3KSC0, J3QMY9, O14603, O93195, O95411, P03414, P0C7M3, P37200, P47939, P47940, P49671, P92561, Q02919, Q32KZ5, Q4G0G2, Q5SR53, Q5T0J3, Q5T6R2, Q66669, Q66HF0, Q6AWC8, Q6DGF6, Q6ZP68, Q6ZSR6, Q7L4S7, Q86UQ5, Q86Y29, Q8BGX4, Q8N326, Q8N4M7, Q8N6C7, Q8N769

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

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	1
Likely pathogenic	0
Uncertain significance	21
Likely benign	3
Benign	0

Top pathogenic / likely-pathogenic (1)

Variant ID	HGVS	Classification
1209858	GRCh37/hg19 Xq21.32-23(chrX:91829757-113050225)x1	Pathogenic

SpliceAI

596 predictions. Top by Δscore:

Variant	Effect	Δscore
X:101616762:TGAAT:T	acceptor_gain	1.0000
X:101616763:GAAT:G	acceptor_gain	1.0000
X:101616764:AAT:A	acceptor_gain	1.0000
X:101616765:AT:A	acceptor_gain	1.0000
X:101616766:TCTG:T	acceptor_loss	1.0000
X:101616767:C:CC	acceptor_gain	1.0000
X:101617498:CTGA:C	donor_loss	0.9900
X:101617499:TGACC:T	donor_loss	0.9900
X:101617500:GA:G	donor_loss	0.9900
X:101617501:AC:A	donor_loss	0.9900
X:101617880:CCGA:C	donor_loss	0.9900
X:101617882:GA:G	donor_loss	0.9900
X:101617883:ACCTG:A	donor_loss	0.9900
X:101617884:CC:C	donor_loss	0.9900
X:101617905:T:A	donor_gain	0.9900
X:101616773:G:GC	acceptor_gain	0.9800
X:101616667:TC:T	donor_gain	0.9700
X:101616668:CC:C	donor_gain	0.9700
X:101616669:C:CT	donor_gain	0.9700
X:101617580:CAAAC:C	acceptor_gain	0.9700
X:101617088:T:TA	donor_gain	0.9600
X:101616773:G:C	acceptor_gain	0.9500
X:101616769:G:C	acceptor_gain	0.9400
X:101616769:G:GC	acceptor_gain	0.9400
X:101617586:T:G	acceptor_loss	0.9400
X:101617881:CGACC:C	donor_gain	0.9400
X:101617582:AAC:A	acceptor_gain	0.9300
X:101617583:AC:A	acceptor_gain	0.9300
X:101617584:CC:C	acceptor_gain	0.9300
X:101617796:G:C	donor_gain	0.9100

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000095926 (X:101616613 C>G,T), RS1000161830 (X:101618087 C>T), RS1000592055 (X:101616282 C>G), RS1004275555 (X:101616981 G>A), RS1004656963 (X:101617281 A>C,G), RS1011235066 (X:101618628 C>T), RS1012069240 (X:101619576 G>A,C,T), RS1012077569 (X:101619277 T>C), RS1013752885 (X:101617311 T>C), RS1015732844 (X:101616763 G>T), RS1019370819 (X:101618785 G>T), RS1022424617 (X:101619697 A>C), RS1023504756 (X:101619578 C>A), RS1023514931 (X:101619288 C>A,G,T), RS1025221492 (X:101617680 C>T)

Disease associations

OMIM: gene MIM:301048 | 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

12 total (human), top 12 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Tobacco Smoke Pollution	increases expression	2
dicrotophos	decreases expression	1
bisphenol A	increases expression	1
perfluorooctane sulfonic acid	increases expression	1
Sunitinib	decreases expression	1
Air Pollutants, Occupational	affects expression	1
Benzo(a)pyrene	increases methylation	1
Doxorubicin	decreases expression	1
Valproic Acid	decreases expression	1
Aflatoxin B1	decreases methylation	1
Copper Sulfate	decreases expression	1
Nanotubes, Carbon	increases expression	1

Clinical trials (associated diseases)

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