MAGIX

Summary

MAGIX (MAGI family member, X-linked, HGNC:30006) is a protein-coding gene on chromosome Xp11.23, encoding PDZ domain-containing protein MAGIX (Q9H6Y5).

At a glance

• Clinical variants (ClinVar): 70 total
• MANE Select transcript: NM_024859

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:30006
Approved symbol	MAGIX
Name	MAGI family member, X-linked
Location	Xp11.23
Locus type	gene with protein product
Status	Approved
Aliases	PDZX, JM10, FLJ21687
Ensembl gene	ENSG00000269313
Ensembl biotype	protein_coding
Entrez	79917

Gene structure

Transcript identifiers

Ensembl transcripts: 10 — 7 protein_coding, 1 protein_coding_CDS_not_defined, 1 nonsense_mediated_decay, 1 retained_intron

ENST00000454342, ENST00000595224, ENST00000612119, ENST00000614074, ENST00000614322, ENST00000615626, ENST00000615915, ENST00000616266, ENST00000616812, ENST00000910545

RefSeq mRNA: 4 — MANE Select: NM_024859 NM_001099681, NM_001099682, NM_001395401, NM_024859

CCDS: CCDS48106, CCDS48107, CCDS75976, CCDS94607

Canonical transcript exons

ENST00000595224 — 6 exons

Exon	Start	End
ENSE00002983203	49164863	49165090
ENSE00002993416	49163783	49163929
ENSE00003067407	49164707	49164789
ENSE00003118143	49165190	49165361
ENSE00003978352	49166074	49168774
ENSE00003978353	49162758	49162938

Expression profiles

Bgee: expression breadth ubiquitous, 175 present calls, max score 85.33.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.0980 / max 6.6753, expressed in 51 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
196316	0.0980	51

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
right lobe of liver	UBERON:0001114	85.33	gold quality
mucosa of transverse colon	UBERON:0004991	83.70	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	83.48	gold quality
cerebellar hemisphere	UBERON:0002245	82.31	gold quality
right hemisphere of cerebellum	UBERON:0014890	82.19	gold quality
cerebellar cortex	UBERON:0002129	82.17	gold quality
body of stomach	UBERON:0001161	81.63	gold quality
right uterine tube	UBERON:0001302	81.56	gold quality
body of pancreas	UBERON:0001150	81.41	gold quality
cerebellum	UBERON:0002037	80.02	gold quality
right atrium auricular region	UBERON:0006631	79.97	gold quality
cardiac atrium	UBERON:0002081	77.47	gold quality
metanephros cortex	UBERON:0010533	76.70	gold quality
stomach	UBERON:0000945	76.69	gold quality
prefrontal cortex	UBERON:0000451	76.42	gold quality
right lobe of thyroid gland	UBERON:0001119	76.38	gold quality
apex of heart	UBERON:0002098	76.28	gold quality
left lobe of thyroid gland	UBERON:0001120	76.12	gold quality
hindlimb stylopod muscle	UBERON:0004252	75.63	gold quality
minor salivary gland	UBERON:0001830	74.95	gold quality
lower esophagus mucosa	UBERON:0035834	74.78	gold quality
pancreas	UBERON:0001264	74.43	gold quality
bronchial epithelial cell	CL:0002328	74.15	gold quality
adenohypophysis	UBERON:0002196	73.89	gold quality
thyroid gland	UBERON:0002046	73.73	gold quality
saliva-secreting gland	UBERON:0001044	73.29	gold quality
anterior cingulate cortex	UBERON:0009835	73.06	gold quality
cingulate cortex	UBERON:0003027	72.96	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	72.81	gold quality
adult mammalian kidney	UBERON:0000082	72.76	gold quality

Single-cell (SCXA)

Detected in 3 experiment(s), a significant marker in 2.

Experiment	Marker?	Max mean expression
E-ANND-3	yes	5.77
E-GEOD-110499	yes	5.74
E-MTAB-6058	no	43.55

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

35 targeting MAGIX, 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-4283	100.00	66.42	2097
HSA-MIR-4455	100.00	65.48	1587
HSA-MIR-5193	100.00	67.26	1744
HSA-MIR-4650-5P	99.98	64.69	999
HSA-MIR-6888-3P	99.97	65.95	1170
HSA-MIR-4267	99.96	66.53	2368
HSA-MIR-4447	99.85	67.81	2900
HSA-MIR-3934-3P	99.76	65.51	1351
HSA-MIR-148A-3P	99.74	73.77	1700
HSA-MIR-148B-3P	99.74	73.75	1700
HSA-MIR-152-3P	99.74	73.75	1703
HSA-MIR-4428	99.73	66.41	1733
HSA-MIR-657	99.48	66.02	848
HSA-MIR-766-3P	99.47	65.24	1811
HSA-MIR-6165	99.44	67.12	1389
HSA-MIR-4667-3P	99.26	65.45	1608
HSA-MIR-5690	99.25	67.58	1012
HSA-MIR-6510-5P	99.14	66.59	1081
HSA-MIR-4326	98.97	67.63	962
HSA-MIR-412-3P	98.86	66.89	712
HSA-MIR-6754-3P	98.84	66.60	889
HSA-MIR-6887-5P	98.56	68.49	1295
HSA-MIR-6795-5P	98.52	68.51	1277
HSA-MIR-7111-3P	97.80	66.75	1467
HSA-MIR-3665	97.73	65.08	975
HSA-MIR-6855-5P	97.51	66.03	830
HSA-MIR-4286	97.20	64.37	1587
HSA-MIR-6869-5P	97.17	67.06	634
HSA-MIR-1306-5P	97.11	64.04	755
HSA-MIR-134-5P	97.11	66.52	976

Cross-species orthologs

6 orthologs

Organism	Symbol	Gene ID
danio_rerio	magixa	ENSDARG00000025108
danio_rerio	magixb	ENSDARG00000077633
mus_musculus	Magix	ENSMUSG00000031147
rattus_norvegicus	Magix	ENSRNOG00000010092
drosophila_melanogaster	Magi	FBGN0034590
caenorhabditis_elegans		WBGENE00010444

Paralogs (6): MAGI3 (ENSG00000081026), GRIP2 (ENSG00000144596), MAGI1 (ENSG00000151276), SAV1 (ENSG00000151748), GRIP1 (ENSG00000155974), MAGI2 (ENSG00000187391)

Protein

Protein identifiers

PDZ domain-containing protein MAGIX — Q9H6Y5 (reviewed: Q9H6Y5)

All UniProt accessions (6): A0A087WUY6, A0A087WW28, A0A087X1L4, A0A087X263, C9J123, Q9H6Y5

Isoforms (3)

UniProt ID	Names	Canonical?
Q9H6Y5-1	1	yes
Q9H6Y5-2	2
Q9H6Y5-3	3

RefSeq proteins (4): NP_001093151, NP_001093152, NP_001382330, NP_079135* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001478	PDZ	Domain
IPR030031	MAGIX	Family
IPR036034	PDZ_sf	Homologous_superfamily

Pfam: PF00595

UniProt features (22 total): strand 6, sequence variant 4, compositionally biased region 3, helix 2, region of interest 2, splice variant 2, chain 1, domain 1, modified residue 1

Structure

Experimental structures (PDB)

1 structures.

PDB	Method	Resolution (Å)
2DJT	SOLUTION NMR

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9H6Y5-F1	61.84	0.24

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): 272

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 56 (showing top): SHETH_LIVER_CANCER_VS_TXNIP_LOSS_PAM4, GTGTGAG_MIR342, TGGAAA_NFAT_Q4_01, AP2_Q6, DODD_NASOPHARYNGEAL_CARCINOMA_DN, CHEN_METABOLIC_SYNDROM_NETWORK, YRCCAKNNGNCGC_UNKNOWN, MIKKELSEN_MEF_HCP_WITH_H3_UNMETHYLATED, chrXp11, ATF2_S_UP.V1_DN, IL2_UP.V1_UP, JAK2_DN.V1_DN, KRAS.300_UP.V1_DN, KRAS.600_UP.V1_DN, KRAS.PROSTATE_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

242 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
MAGIX	LNX2	Q8N448	370
MAGIX	PEX14	O75381	370
MAGIX	ARL4C	P56559	316
MAGIX	APBA3	O96018	244
MAGIX	GAK	O14976	210
MAGIX	PARD6G	Q9BYG4	209
MAGIX	PDZD11	Q5EBL8	204
MAGIX	DNAJC22	Q8N4W6	204
MAGIX	ABT1	Q9ULW3	196
MAGIX	MYO7B	Q6PIF6	192
MAGIX	PARD6A	Q9NPB6	190
MAGIX	SNTG1	Q9NSN8	186
MAGIX	BRD7	Q9NPI1	173
MAGIX	BRD9	Q9H8M2	173
MAGIX	JTB	O76095	167
MAGIX	MAGI3	Q5TCQ9	167

IntAct

27 interactions, top by confidence:

A	B	Type	Score
SLCO1C1	MAGIX	psi-mi:“MI:0407”(direct interaction)	0.440
E6	MAGIX	psi-mi:“MI:0407”(direct interaction)	0.440
ABCC4	MAGIX	psi-mi:“MI:0407”(direct interaction)	0.440
ARHGEF16	MAGIX	psi-mi:“MI:0407”(direct interaction)	0.440
ASIC3	MAGIX	psi-mi:“MI:0407”(direct interaction)	0.440
ATP2B4	MAGIX	psi-mi:“MI:0407”(direct interaction)	0.440
CYSLTR2	MAGIX	psi-mi:“MI:0407”(direct interaction)	0.440
DGKK	MAGIX	psi-mi:“MI:0407”(direct interaction)	0.440
DGKZ	MAGIX	psi-mi:“MI:0407”(direct interaction)	0.440
DOCK4	MAGIX	psi-mi:“MI:0407”(direct interaction)	0.440
FRMPD4	MAGIX	psi-mi:“MI:0407”(direct interaction)	0.440
FZD7	MAGIX	psi-mi:“MI:0407”(direct interaction)	0.440
MAGIX	TAMALIN	psi-mi:“MI:0407”(direct interaction)	0.440
ORF putative E6	MAGIX	psi-mi:“MI:0407”(direct interaction)	0.440
KCNA5	MAGIX	psi-mi:“MI:0407”(direct interaction)	0.440
KIR3DL3	MAGIX	psi-mi:“MI:0407”(direct interaction)	0.440
MAP2K2	MAGIX	psi-mi:“MI:0407”(direct interaction)	0.440
MAGIX	PBK	psi-mi:“MI:0407”(direct interaction)	0.440
RALBP1	MAGIX	psi-mi:“MI:0407”(direct interaction)	0.440
RASSF6	MAGIX	psi-mi:“MI:0407”(direct interaction)	0.440
SLC15A5	MAGIX	psi-mi:“MI:0407”(direct interaction)	0.440
TJP2	MAGIX	psi-mi:“MI:0407”(direct interaction)	0.440
MAGIX	ERCC1	psi-mi:“MI:0914”(association)	0.350
MAGIX	CLUH	psi-mi:“MI:0914”(association)	0.350

BioGRID (68): CDC27 (Affinity Capture-MS), CDC23 (Affinity Capture-MS), STK24 (Affinity Capture-MS), STK26 (Affinity Capture-MS), TJP1 (Affinity Capture-MS), ANAPC5 (Affinity Capture-MS), ANAPC7 (Affinity Capture-MS), MCMBP (Affinity Capture-MS), DGKH (Affinity Capture-MS), CDC16 (Affinity Capture-MS), ANAPC4 (Affinity Capture-MS), PMPCA (Affinity Capture-MS), ANAPC1 (Affinity Capture-MS), PMPCB (Affinity Capture-MS), NCAPH (Affinity Capture-MS)

ESM2 similar proteins: A0A1W2PPE3, A0A2R8Y2Y2, A0A494C0N9, A0A494C0Y3, A0A7I2V3R4, A0JNN8, A2VDX9, A5A769, A5PJP1, A6QPM6, A8MTW9, C9JTQ0, O15370, O35182, O43541, O70218, O75474, O89113, O94850, P0C7X2, P0DPE3, P28283, P37318, P37319, P70339, Q04890, Q10586, Q32PF6, Q5BLP8, Q5T230, Q5U5M8, Q5VY09, Q60925, Q6IQX8, Q6NZ36, Q6NZY7, Q6QNY0, Q6ZSJ8, Q7TNS8, Q80WY3

Diamond homologs: A0A0G2K2P5, A0A8P0N4K0, C5IAW9, F1LW30, O08721, O08722, O08747, O62683, O95049, O95185, O97758, P39447, P57105, Q07157, Q0P5E6, Q13424, Q28626, Q32LE7, Q3T0C9, Q5EBL8, Q5ZIK2, Q61234, Q6NXB2, Q6QA76, Q6R653, Q6UXZ4, Q6ZN44, Q761X5, Q7KRY7, Q7T2Z5, Q80VW5, Q86UL8, Q8IV45, Q8IZJ1, Q8JGT4, Q8K1S2, Q8K1S3, Q8K1S4, Q95168, Q9CZG9

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	23
Likely benign	1
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1049 predictions. Top by Δscore:

Variant	Effect	Δscore
X:49163925:GGAGG:G	donor_gain	1.0000
X:49163926:GAGG:G	donor_gain	1.0000
X:49163926:GAGGG:G	donor_gain	1.0000
X:49163927:AGG:A	donor_gain	1.0000
X:49163928:GG:G	donor_gain	1.0000
X:49163928:GGG:G	donor_gain	1.0000
X:49163929:GG:G	donor_gain	1.0000
X:49163930:G:C	donor_loss	1.0000
X:49163930:G:GG	donor_gain	1.0000
X:49163931:T:A	donor_loss	1.0000
X:49164702:CCCA:C	acceptor_loss	1.0000
X:49164703:CCA:C	acceptor_loss	1.0000
X:49164705:A:AG	acceptor_gain	1.0000
X:49164706:G:GA	acceptor_gain	1.0000
X:49164706:GCT:G	acceptor_gain	1.0000
X:49163922:G:GT	donor_gain	0.9900
X:49163927:A:T	donor_gain	0.9900
X:49164699:T:G	acceptor_gain	0.9900
X:49164702:CCCAG:C	acceptor_gain	0.9900
X:49164703:CCAG:C	acceptor_gain	0.9900
X:49164704:CAGC:C	acceptor_gain	0.9900
X:49164705:AGCT:A	acceptor_gain	0.9900
X:49164705:AGCTG:A	acceptor_gain	0.9900
X:49164706:GC:G	acceptor_gain	0.9900
X:49164706:GCTG:G	acceptor_gain	0.9900
X:49164706:GCTGT:G	acceptor_gain	0.9900
X:49164785:CCCAG:C	donor_loss	0.9900
X:49164786:CCAGG:C	donor_loss	0.9900
X:49164787:CAGGT:C	donor_loss	0.9900
X:49164788:AG:A	donor_loss	0.9900

AlphaMissense

2093 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
X:49164986:T:C	F135L	0.983
X:49164988:T:A	F135L	0.983
X:49164988:T:G	F135L	0.983
X:49165197:A:T	D172V	0.969
X:49165263:T:C	I194T	0.966
X:49165197:A:G	D172G	0.961
X:49165215:A:T	N178I	0.961
X:49165086:T:C	L168S	0.956
X:49165197:A:C	D172A	0.951
X:49165198:C:A	D172E	0.946
X:49165198:C:G	D172E	0.946
X:49165196:G:C	D172H	0.944
X:49165212:T:C	I177T	0.944
X:49164953:T:C	F124L	0.936
X:49164955:C:A	F124L	0.936
X:49164955:C:G	F124L	0.936
X:49165250:G:C	A190P	0.936
X:49164987:T:C	F135S	0.934
X:49165216:C:A	N178K	0.932
X:49165216:C:G	N178K	0.932
X:49165212:T:A	I177N	0.928
X:49165212:T:G	I177S	0.928
X:49165203:T:A	V174E	0.921
X:49165296:T:A	I205N	0.905
X:49166301:T:A	W303R	0.905
X:49166301:T:C	W303R	0.905
X:49165296:T:G	I205S	0.900
X:49165263:T:G	I194S	0.892
X:49165296:T:C	I205T	0.889
X:49165290:T:C	L203P	0.888

dbSNP variants (sampled 300 via entrez): RS1000385177 (X:49161858 C>T), RS1002335630 (X:49167353 C>A), RS1002723109 (X:49169175 A>C), RS1004637469 (X:49161225 G>T), RS1009085527 (X:49162681 T>C), RS1009471471 (X:49165455 G>A), RS1009550924 (X:49162301 G>A), RS1009834305 (X:49165902 G>A,T), RS1011562875 (X:49167449 A>G), RS1013322257 (X:49165033 G>A), RS1013412698 (X:49161730 C>T), RS1014702398 (X:49162779 G>C,T), RS1016315731 (X:49166453 G>A), RS1016657726 (X:49168020 T>C,G), RS1016778239 (X:49165975 T>C)

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

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

20 total (human), top 20 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Benzo(a)pyrene	affects methylation, decreases expression, decreases methylation, increases methylation	2
Smoke	increases abundance, increases expression	2
GSK-J4	decreases expression	1
aminomethylphosphonic acid (AMPA)	decreases expression	1
cinnamaldehyde	increases expression	1
ferrous chloride	decreases expression	1
abrine	increases expression	1
jinfukang	increases expression	1
Sunitinib	increases expression	1
Air Pollutants	increases abundance, increases expression	1
Arsenic	increases methylation	1
Coal	increases abundance, increases expression	1
Lead	increases expression	1
Methotrexate	increases expression	1
Methyl Methanesulfonate	increases expression	1
Niclosamide	increases expression	1
Tetrachlorodibenzodioxin	increases expression	1
2,4-Dichlorophenoxyacetic Acid	decreases expression	1
Antirheumatic Agents	increases expression	1
Acrylamide	increases expression	1

Clinical trials (associated diseases)

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