MID1

Summary

MID1 (midline 1, HGNC:7095) is a protein-coding gene on chromosome Xp22.2, encoding E3 ubiquitin-protein ligase Midline-1 (O15344). Has E3 ubiquitin ligase activity towards IGBP1, promoting its monoubiquitination, which results in deprotection of the catalytic subunit of protein phosphatase PP2A, and its subsequent degradation by polyubiquitination. It is haploinsufficient (ClinGen: sufficient evidence).

The protein encoded by this gene is a member of the tripartite motif (TRIM) family, also known as the ‘RING-B box-coiled coil’ (RBCC) subgroup of RING finger proteins. The TRIM motif includes three zinc-binding domains, a RING, a B-box type 1 and a B-box type 2, and a coiled-coil region. This protein forms homodimers which associate with microtubules in the cytoplasm. The protein is likely involved in the formation of multiprotein structures acting as anchor points to microtubules. Mutations in this gene have been associated with the X-linked form of Opitz syndrome, which is characterized by midline abnormalities such as cleft lip, laryngeal cleft, heart defects, hypospadias, and agenesis of the corpus callosum. This gene was also the first example of a gene subject to X inactivation in human while escaping it in mouse. Alternative promoter use, alternative splicing and alternative polyadenylation result in multiple transcript variants that have different tissue specificities.

Source: NCBI Gene 4281 — RefSeq curated summary.

At a glance

• Gene–disease (curated): X-linked Opitz G/BBB syndrome (Definitive, ClinGen)
• Clinical variants (ClinVar): 529 total — 45 pathogenic, 23 likely-pathogenic
• Phenotypes (HPO): 96
• Dosage sensitivity (ClinGen): haploinsufficiency sufficient evidence, triplosensitivity no evidence
• MANE Select transcript: NM_000381

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:7095
Approved symbol	MID1
Name	midline 1
Location	Xp22.2
Locus type	gene with protein product
Status	Approved
Aliases	OS, FXY, TRIM18, RNF59
Ensembl gene	ENSG00000101871
Ensembl biotype	protein_coding
OMIM	300552
Entrez	4281

Gene structure

Transcript identifiers

Ensembl transcripts: 25 — 16 protein_coding, 5 retained_intron, 4 protein_coding_CDS_not_defined

ENST00000317552, ENST00000380779, ENST00000380780, ENST00000380782, ENST00000380785, ENST00000380787, ENST00000413894, ENST00000453318, ENST00000479925, ENST00000610939, ENST00000616003, ENST00000674917, ENST00000675073, ENST00000675358, ENST00000686012, ENST00000687008, ENST00000689180, ENST00000689773, ENST00000689988, ENST00000690004, ENST00000691913, ENST00000691943, ENST00000693721, ENST00000707197, ENST00000707198

RefSeq mRNA: 9 — MANE Select: NM_000381 NM_000381, NM_001098624, NM_001193277, NM_001193278, NM_001193279, NM_001193280, NM_001347733, NM_033289, NM_033290

CCDS: CCDS14138, CCDS75952, CCDS94548, CCDS94549

Canonical transcript exons

ENST00000317552 — 10 exons

Exon	Start	End
ENSE00000665013	10474623	10474750
ENSE00000665015	10482480	10482628
ENSE00000854562	10495584	10495691
ENSE00001142388	10459646	10459807
ENSE00001195785	10523092	10523187
ENSE00001276841	10566888	10567603
ENSE00001486255	10445556	10449716
ENSE00001620590	10620290	10620585
ENSE00001661606	10469697	10469840
ENSE00003463858	10454870	10455077

Expression profiles

Bgee: expression breadth ubiquitous, 283 present calls, max score 98.00.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 15.9434 / max 270.0191, expressed in 1452 samples.

FANTOM5 promoters (21 alternative TSS)

Promoter ID	TPM avg	Samples expressed
198395	4.8765	1163
198393	3.0454	991
198394	2.2579	871
198404	1.0968	412
198386	0.9410	225
198405	0.8071	362
198410	0.6574	384
198401	0.4608	144
198406	0.3255	155
198391	0.2891	136

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
mucosa of paranasal sinus	UBERON:0005030	98.00	gold quality
ventricular zone	UBERON:0003053	97.63	gold quality
cervix squamous epithelium	UBERON:0006922	97.32	gold quality
pancreatic ductal cell	CL:0002079	96.98	gold quality
hair follicle	UBERON:0002073	96.29	gold quality
bronchial epithelial cell	CL:0002328	95.06	gold quality
epithelium of bronchus	UBERON:0002031	94.44	gold quality
bronchus	UBERON:0002185	94.21	gold quality
seminal vesicle	UBERON:0000998	94.09	gold quality
tongue squamous epithelium	UBERON:0006919	93.98	gold quality
heart right ventricle	UBERON:0002080	93.23	gold quality
choroid plexus epithelium	UBERON:0003911	92.60	gold quality
ganglionic eminence	UBERON:0004023	92.12	gold quality
mucosa of urinary bladder	UBERON:0001259	92.10	gold quality
pigmented layer of retina	UBERON:0001782	91.99	gold quality
squamous epithelium	UBERON:0006914	91.68	gold quality
secondary oocyte	CL:0000655	91.62	gold quality
tibia	UBERON:0000979	91.16	gold quality
cauda epididymis	UBERON:0004360	91.06	gold quality
mammalian vulva	UBERON:0000997	91.01	gold quality
buccal mucosa cell	CL:0002336	90.99	gold quality
vena cava	UBERON:0004087	90.94	gold quality
visceral pleura	UBERON:0002401	90.85	gold quality
oocyte	CL:0000023	90.73	gold quality
embryo	UBERON:0000922	90.47	gold quality
gingiva	UBERON:0001828	90.46	gold quality
gingival epithelium	UBERON:0001949	90.29	gold quality
esophagus squamous epithelium	UBERON:0006920	90.09	gold quality
urethra	UBERON:0000057	90.04	gold quality
saphenous vein	UBERON:0007318	89.83	gold quality

Single-cell (SCXA)

Detected in 5 experiment(s), a significant marker in 3.

Experiment	Marker?	Max mean expression
E-CURD-119	yes	32.53
E-GEOD-93593	yes	14.23
E-ANND-3	yes	11.80
E-MTAB-8894	no	349.83
E-GEOD-99795	no	115.17

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): AR

miRNA regulators (miRDB)

183 targeting MID1, 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-5692A	100.00	74.40	6850
HSA-MIR-3613-3P	100.00	76.36	7965
HSA-MIR-3646	100.00	73.56	5283
HSA-MIR-1277-5P	100.00	73.95	5056
HSA-MIR-3163	100.00	77.23	8605
HSA-MIR-4476	100.00	68.18	2030
HSA-MIR-6876-5P	100.00	67.68	2126
HSA-MIR-4768-5P	100.00	69.49	2861
HSA-MIR-6833-3P	100.00	70.63	3197
HSA-MIR-340-5P	100.00	72.50	4437
HSA-MIR-4533	100.00	69.48	2758
HSA-MIR-548AW	99.99	72.57	3559
HSA-MIR-3662	99.99	73.82	5684
HSA-MIR-1184	99.99	68.19	1458
HSA-MIR-186-5P	99.99	70.83	3707
HSA-MIR-34A-5P	99.99	71.21	1784
HSA-MIR-449A	99.99	71.05	1776
HSA-MIR-33B-5P	99.99	68.58	1062
HSA-MIR-4534	99.99	66.58	1907
HSA-MIR-19A-3P	99.98	75.33	2762
HSA-MIR-19B-3P	99.98	75.44	2754
HSA-MIR-548AN	99.97	70.91	2817
HSA-MIR-1468-3P	99.96	72.74	3797
HSA-MIR-548AJ-3P	99.96	73.38	5345
HSA-MIR-548X-3P	99.96	73.38	5345
HSA-MIR-9-3P	99.96	70.88	2068
HSA-MIR-548AA	99.96	70.64	3753
HSA-MIR-548AP-3P	99.96	70.64	3753
HSA-MIR-548T-3P	99.96	70.64	3753
HSA-MIR-767-5P	99.95	70.85	993

Functional genomics

ClinGen dosage: haploinsufficiency 3 (sufficient evidence), triplosensitivity 0 (no evidence). ClinGen Gene Dosage Map

Literature-anchored findings (GeneRIF, showing 40)

• PP2Ac accumulation is caused by an impairment of a newly identified E3 ubiquitin ligase activity of the MID1 protein (PMID:11685209)
• MID1 coiled-coil motifs mediate both homo- and heterodimerization, a prerequisite for association of the MID-alpha 4 complex with microtubules. (PMID:11806752)
• Widely spaced alternative promoters, conserved between human and rodent, control the expression of Mid1 (PMID:12408967)
• Mid1 is transcribed from a human endogenous retroviral promoter (PMID:12411602)
• These searches revealed a fusion transcript containing the LTR of an HERV-E element linked to the Opitz syndrome gene Mid1 (PMID:12411602)
• identified a duplication of the MID1 first exon in a patient with X-linked Opitz G/BBB syndrome (PMID:12545276)
• The Opitz syndrome gene MID1 is essential for establishing asymmetric gene expression in Hensen’s node. (PMID:12798296)
• Novel mutations are described in the MID1 gene, particularly in the 3’ flanking region. (PMID:12833403)
• FibronectinIII domain of the MID1 protein may be involved in midline differentiation after neural tube and palatal structures are completed. (PMID:16378742)
• a novel insertion mutation (c.1798_1799-insC)in MID1 gene was identified; first report on a genetically confirmed case of X-linked Opitz G/BBB syndrome in Korea (PMID:17043407)
• Twenty-nine novel mutations are associated with Opitz G/BBB Syndrome. (PMID:17221865)
• The tertiary structure of the B-box2 (CHC(D/C)C(2)H(2)) domain from MID1, is reported using multidimensional nuclear magnetic resonance spectroscopy. (PMID:17428496)
• the apparent occurrence of an unusual TG 3’ splice site in intron 9 is discussed (PMID:17672918)
• MID1 expression is tightly regulated through concerted action of alternative promoters and alternative polyadenylation signals both during embryonic development and in the adult. (PMID:18005432)
• Mutant MID1 proteins cannot bind EF-1alpha and results in the development of the ventral midline in Opitz syndrome patients (PMID:18172692)
• Structure of the MID1 tandem B-boxes reveals an interaction reminiscent of intermolecular ring heterodimers. (PMID:18220417)
• reviewed all the MID1 mutations reported so far, in both familial and sporadic cases. The mutations are scattered along the entire length of the gene (PMID:18360914)
• A new MID1 mutation leading to a premature stop codon was found in patients with Opitz G/BBB syndrome. (PMID:18697196)
• Active transport of the ubiquitin ligase MID1 along the microtubules is regulated by protein phosphatase 2A. (PMID:18949047)
• Non-random tranmission of MID1 haplotypes in male non-syndromic cleft lip with or without cleft palate patients was observed. (PMID:19049519)
• These studies shed light on MID1 E3 ligase activity and show how its three zinc-binding domains can contribute to MID1’s overall function. (PMID:21296087)
• Our finding suggests that hypospadias associated with hypertelorism is the mildest phenotype in OS caused by MID1 mutations. (PMID:21326312)
• mTORC1 signaling as a downstream pathway regulated by the MID1/PP2A axis, suggesting that mTORC1 plays a key role in Opitz syndrome pathogenesis. (PMID:21555591)
• Protein phosphatase 2A (PP2A)-specific ubiquitin ligase MID1 is a sequence-dependent regulator of translation efficiency controlling 3-phosphoinositide-dependent protein kinase-1 (PDPK-1). (PMID:21930711)
• found that MID1 was upregulated in primary human bronchial epithelial cells (PMID:23334847)
• expanded CAG repeats bind to a translation regulatory protein complex containing MID1, protein phosphatase 2A and 40S ribosomal S6 kinase. (PMID:23443539)
• for the first time within the MID1 gene, a complex rearrangement composed of two deletions, an inversion and a small insertion that may suggest the involvement of concurrent non-homologous mechanisms in the generation of the observed structural variant. (PMID:23791568)
• Two patients with underdeveloped arcuate fasciculus had novel, nonsynonymous variants in MID1 and EN2 genes regulating axon guidance pathway. (PMID:24321989)
• In prostate cancer cells the inhibitory effect of metformin was mimicked by disruption of MID1 translational regulator complex. (PMID:24484909)
• Promotion of AR, in addition to enhancement of the Akt-, NFkappaB-, and Hh-pathways by sustained MID1-upregulation during androgen deprivation therapy provides a powerful proliferative scenario for PCa progression into castration resistance (PMID:24913494)
• MID1 catalyzes the ubiquitination of protein phosphatase 2A and mutations within its Bbox1 domain disrupt polyubiquitination of alpha4 but not of PP2Ac in X-linked Opitz syndrome. (PMID:25207814)
• These studies provide insight into the mechanism by which mutations observed in X-linked Opitz G syndrome affect the structure and function of the MID1 Bbox1 domain (PMID:25216264)
• Fu ubiquitination and cleavage is one of the key elements connecting the MID1-PP2A protein complex with GLI3 activity control (PMID:25278022)
• A familial c.1102C>T (p.R368X) mutation in the MID1 gene, is reported. (PMID:25304119)
• Results revealed S422 as a novel phosphorylation site of Osx and GSK-3b played an important role in regulating the protein stability and transactivational activity of Osx. (PMID:25728276)
• A130T/V mutations within the MID1 zinc-binding Bbox1 domain affects protein folding. (PMID:25874572)
• TRAIL regulates MID1 and TSLP, inflammation, fibrosis, smooth muscle hypertrophy, and expression of inflammatory effector chemokines and cytokines in experimental eosinophilic esophagitis. (PMID:25981737)
• the coiled-coil and COS domain (CC-COS) bind to microtubules, demonstrating for the first time that MID1 can directly associate with the microtubules (PMID:27367845)
• Osx is upregulated in patients with Ossification of the posterior longitudinal ligament. (PMID:27693496)
• P151L MID1 mutation is associated with X-linked Opitz Syndrome. (PMID:28548391)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	mid1	ENSDARG00000060482
mus_musculus	Mid1	ENSMUSG00000035299
rattus_norvegicus	Mid1	ENSRNOG00000003613

Paralogs (80): MID2 (ENSG00000080561), TRIM9 (ENSG00000100505), MEFV (ENSG00000103313), TRIM35 (ENSG00000104228), TRIM14 (ENSG00000106785), TRIM37 (ENSG00000108395), TRIM2 (ENSG00000109654), TRIM3 (ENSG00000110171), TRIM38 (ENSG00000112343), TRIM62 (ENSG00000116525), TRIM67 (ENSG00000119283), TRIM32 (ENSG00000119401), BSPRY (ENSG00000119411), TRIM25 (ENSG00000121060), TRIM6 (ENSG00000121236), TRIM24 (ENSG00000122779), TRIM51 (ENSG00000124900), TRIM28 (ENSG00000130726), TRIM21 (ENSG00000132109), TRIM5 (ENSG00000132256), TRIM22 (ENSG00000132274), TRIM47 (ENSG00000132481), TRIM45 (ENSG00000134253), TRIM29 (ENSG00000137699), TRIM54 (ENSG00000138100), PML (ENSG00000140464), TRIM65 (ENSG00000141569), TRIM43B (ENSG00000144010), TRIM43 (ENSG00000144015), TRIM7 (ENSG00000146054), TRIM41 (ENSG00000146063), TRIM50 (ENSG00000146755), TRIM4 (ENSG00000146833), TRIM55 (ENSG00000147573), TRIM48 (ENSG00000150244), TRIM36 (ENSG00000152503), TRIM11 (ENSG00000154370), TRIM74 (ENSG00000155428), TRIM42 (ENSG00000155890), TRIM63 (ENSG00000158022)

Protein

Protein identifiers

E3 ubiquitin-protein ligase Midline-1 — O15344 (reviewed: O15344)

Alternative names: Midin, Putative transcription factor XPRF, RING finger protein 59, RING finger protein Midline-1, RING-type E3 ubiquitin transferase Midline-1, Tripartite motif-containing protein 18

All UniProt accessions (9): O15344, A0A087X255, A0A6Q8PF94, A0A6Q8PGA5, A0A6Q8PGE7, A0A8I5KPB2, A0A8I5KPE0, A0A8I5KR14, C9J453

UniProt curated annotations — full annotation on UniProt →

Function. Has E3 ubiquitin ligase activity towards IGBP1, promoting its monoubiquitination, which results in deprotection of the catalytic subunit of protein phosphatase PP2A, and its subsequent degradation by polyubiquitination.

Subunit / interactions. Homodimer or heterodimer with MID2. Interacts with IGBP1. Interacts with TRIM16.

Subcellular location. Cytoplasm. Cytoskeleton. Spindle.

Tissue specificity. In the fetus, highest expression found in kidney, followed by brain and lung. Expressed at low levels in fetal liver. In the adult, most abundant in heart, placenta and brain.

Post-translational modifications. Phosphorylated on serine and threonine residues.

Disease relevance. Opitz GBBB syndrome (GBBB) [MIM:300000] A congenital midline malformation syndrome characterized by hypertelorism, genital-urinary defects such as hypospadias in males and splayed labia in females, cleft lip/palate, laryngotracheoesophageal abnormalities, imperforate anus, developmental delay and congenital heart defects. The disease is caused by variants affecting the gene represented in this entry. MID1 mutations produce proteins with a decreased affinity for microtubules.

Induction. A retroviral element acts as an alternative tissue-specific promoter for this gene. The LTR of an HERV-E element enhances the expression in placenta and embryonic kidney.

Similarity. Belongs to the TRIM/RBCC family.

Isoforms (2)

UniProt ID	Names	Canonical?
O15344-1	1, Alpha	yes
O15344-2	2, Beta

RefSeq proteins (9): NP_000372, NP_001092094, NP_001180206, NP_001180207, NP_001180208, NP_001180209, NP_001334662, NP_150631, NP_150632 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR000315	Znf_B-box	Domain
IPR001841	Znf_RING	Domain
IPR001870	B30.2/SPRY	Domain
IPR003649	Bbox_C	Domain
IPR003877	SPRY_dom	Domain
IPR003879	Butyrophylin_SPRY	Domain
IPR003961	FN3_dom	Domain
IPR013083	Znf_RING/FYVE/PHD	Homologous_superfamily
IPR013320	ConA-like_dom_sf	Homologous_superfamily
IPR013783	Ig-like_fold	Homologous_superfamily
IPR017903	COS_domain	Domain
IPR017907	Znf_RING_CS	Conserved_site
IPR027370	Znf-RING_euk	Domain
IPR027727	MID1_Bbox2_Zfn	Domain
IPR036116	FN3_sf	Homologous_superfamily
IPR040859	Midline-1_COS	Domain
IPR043136	B30.2/SPRY_sf	Homologous_superfamily
IPR047095	MID1_Bbox1_Zfn	Domain
IPR050617	E3_ligase_FN3/SPRY	Family

Pfam: PF00041, PF00622, PF00643, PF13445, PF18568, PF22586

UniProt features (69 total): strand 24, binding site 12, sequence variant 7, helix 5, turn 4, domain 3, modified residue 3, zinc finger region 3, compositionally biased region 2, sequence conflict 2, chain 1, splice variant 1, region of interest 1, coiled-coil region 1

Structure

Experimental structures (PDB)

5 structures.

PDB	Method	Resolution (Å)
7QRY	X-RAY DIFFRACTION	2.07
2DQ5	SOLUTION NMR
2FFW	SOLUTION NMR
2JUN	SOLUTION NMR
5IM8	SOLUTION NMR

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-O15344-F1	86.51	0.60

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Ligand- & substrate-binding residues (12): 119; 122; 134; 137; 142; 145; 150; 159; 175; 178; 198; 204

Post-translational modifications (3): 92, 96, 511

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

ID	Pathway
R-HSA-877300	Interferon gamma signaling

MSigDB gene sets: 550 (showing top): GOBP_PROTEIN_LOCALIZATION_TO_CYTOSKELETON, FREAC2_01, TAATAAT_MIR126, GOBP_REGULATION_OF_MICROTUBULE_BASED_PROCESS, GOBP_REGULATION_OF_STRESS_ACTIVATED_PROTEIN_KINASE_SIGNALING_CASCADE, REACTOME_CYTOKINE_SIGNALING_IN_IMMUNE_SYSTEM, GAANYNYGACNY_UNKNOWN, GGGNRMNNYCAT_UNKNOWN, GOBP_POSITIVE_REGULATION_OF_MAPK_CASCADE, GCAAGGA_MIR502, LHX3_01, AAAYRNCTG_UNKNOWN, CAGCTG_AP4_Q5, GOBP_POSITIVE_REGULATION_OF_STRESS_ACTIVATED_PROTEIN_KINASE_SIGNALING_CASCADE, SRF_Q5_01

GO Biological Process (7): microtubule cytoskeleton organization (GO:0000226), negative regulation of microtubule depolymerization (GO:0007026), pattern specification process (GO:0007389), positive regulation of stress-activated MAPK cascade (GO:0032874), protein localization to microtubule (GO:0035372), regulation of microtubule cytoskeleton organization (GO:0070507), positive regulation of intracellular signal transduction (GO:1902533)

GO Molecular Function (11): microtubule binding (GO:0008017), zinc ion binding (GO:0008270), enzyme binding (GO:0019899), ubiquitin protein ligase binding (GO:0031625), identical protein binding (GO:0042802), protein homodimerization activity (GO:0042803), phosphoprotein binding (GO:0051219), ubiquitin protein ligase activity (GO:0061630), protein binding (GO:0005515), transferase activity (GO:0016740), metal ion binding (GO:0046872)

GO Cellular Component (11): cytoplasm (GO:0005737), Golgi apparatus (GO:0005794), spindle (GO:0005819), cytosol (GO:0005829), microtubule (GO:0005874), microtubule associated complex (GO:0005875), centriolar satellite (GO:0034451), cytoskeleton (GO:0005856), cytoplasmic microtubule (GO:0005881), microtubule cytoskeleton (GO:0015630), membrane (GO:0016020)

Reactome top-level categories

Rollup of top-1 pathways:

Category	Pathways
Interferon Signaling	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	4
protein binding	3
cytoplasm	3
microtubule cytoskeleton	3
intracellular membraneless organelle	2
cytoskeleton organization	1
microtubule-based process	1
microtubule depolymerization	1
negative regulation of microtubule polymerization or depolymerization	1
regulation of microtubule depolymerization	1
negative regulation of protein depolymerization	1
negative regulation of supramolecular fiber organization	1
multicellular organism development	1
multicellular organismal process	1
regulation of stress-activated MAPK cascade	1
positive regulation of MAPK cascade	1
stress-activated MAPK cascade	1
positive regulation of stress-activated protein kinase signaling cascade	1
protein localization to microtubule cytoskeleton	1
microtubule cytoskeleton organization	1
regulation of microtubule-based process	1
regulation of cytoskeleton organization	1
positive regulation of signal transduction	1
intracellular signal transduction	1
regulation of intracellular signal transduction	1
tubulin binding	1
transition metal ion binding	1
ubiquitin-like protein ligase binding	1
identical protein binding	1
protein dimerization activity	1
ubiquitin-protein transferase activity	1
ubiquitin-like protein ligase activity	1
binding	1
catalytic activity	1
cation binding	1
intracellular anatomical structure	1
endomembrane system	1
intracellular membrane-bounded organelle	1
polymeric cytoskeletal fiber	1
protein-containing complex	1

Protein interactions and networks

STRING

676 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
MID1	BBOX1	O75936	798
MID1	PPP2CA	P05323	782
MID1	CLCN4	P51793	667
MID1	TRAT1	Q6PIZ9	646
MID1	AMELX	Q99217	638
MID1	EEF1A1	P04719	633
MID1	TMLHE	Q9NVH6	582
MID1	MID1IP1	Q9NPA3	555
MID1	IGBP1	P78318	554
MID1	RACK1	P25388	552
MID1	ANXA2	P07355	548
MID1	PLAC1	Q9HBJ0	466
MID1	PML	P29590	452
MID1	MID2	Q9UJV3	451
MID1	ASMT	P46597	446

IntAct

205 interactions, top by confidence:

A	B	Type	Score
IGBP1	PPP6C	psi-mi:“MI:0914”(association)	0.940
UBE2E2	MID1	psi-mi:“MI:0915”(physical association)	0.870
MID1	UBE2E2	psi-mi:“MI:0915”(physical association)	0.870
UBE2D3	MID1	psi-mi:“MI:0915”(physical association)	0.830
UBE2E3	MID1	psi-mi:“MI:0915”(physical association)	0.830
MID1	UBE2D3	psi-mi:“MI:0915”(physical association)	0.830
MID1	UBE2E3	psi-mi:“MI:0915”(physical association)	0.830
MID1	MID2	psi-mi:“MI:0915”(physical association)	0.810
MID2	MID1	psi-mi:“MI:0915”(physical association)	0.810
MID1	MID1	psi-mi:“MI:0915”(physical association)	0.800

BioGRID (280): PPP2CA (Biochemical Activity), UBE2D1 (Reconstituted Complex), UBE2D2 (Reconstituted Complex), UBE2D3 (Reconstituted Complex), UBE2E1 (Reconstituted Complex), MID1 (Biochemical Activity), PPP2R4 (Biochemical Activity), STK36 (Affinity Capture-Western), STK36 (Biochemical Activity), UBE2D1 (Reconstituted Complex), UBE2D2 (Reconstituted Complex), UBE2D3 (Reconstituted Complex), MID1 (Two-hybrid), MID1 (Two-hybrid), MID1 (Two-hybrid)

ESM2 similar proteins: A1L4K1, D4A7V9, E9QHE3, F1LW30, H0UZ81, O15344, O70583, O95361, P82457, P82458, P97573, Q14258, Q14596, Q28CB1, Q38HM4, Q3UMR0, Q3V3A7, Q58D15, Q5F479, Q5R760, Q5RC94, Q5REJ9, Q5REW9, Q5RF77, Q5XIH6, Q61510, Q6P549, Q6P6S3, Q6UXZ4, Q7T2L7, Q7TNH6, Q7Z494, Q80VK6, Q80WG7, Q8BZ52, Q8JZL1, Q8K1S2, Q8NFM7, Q91Z63, Q969Q1

Diamond homologs: A0A3B3IT33, A6NCK2, A6NDI0, A6NGJ6, A6NI03, A6NLI5, B0BLU1, C9J1S8, I1YAP6, O00478, O00481, O15344, O75677, O75678, O75679, O76064, P0CI25, P0CI26, P18892, P19474, P62603, P86448, P86449, Q13410, Q2HJ46, Q3C1V9, Q3TL54, Q4KLN8, Q5EBN2, Q5PQN2, Q5R4I2, Q5R996, Q61510, Q62556, Q6INS5, Q6MFY8, Q6UX41, Q6UXE8, Q6ZWI9, Q7T308

SIGNOR signaling

5 interactions.

A	Effect	B	Mechanism
Ub:E2	“up-regulates activity”	MID1	ubiquitination
MID1	“down-regulates quantity by destabilization”	PPP2CA	ubiquitination
MID1	“down-regulates quantity by destabilization”	HMG20B	polyubiquitination
MID1	“down-regulates quantity”	PTPN1	ubiquitination
PAK1	“up-regulates activity”	MID1	phosphorylation

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 72 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
TICAM1, RIP1-mediated IKK complex recruitment	5	69.9×	5e-07
Synthesis of active ubiquitin: roles of E1 and E2 enzymes	8	68.5×	4e-11
IKK complex recruitment mediated by RIP1	5	57.7×	1e-06
PINK1-PRKN Mediated Mitophagy	5	41.5×	5e-06
Negative regulators of DDX58/IFIH1 signaling	5	37.9×	6e-06
E3 ubiquitin ligases ubiquitinate target proteins	6	27.0×	4e-06
Antigen processing: Ubiquitination & Proteasome degradation	14	12.1×	4e-10

GO biological processes:

GO term	Partners	Fold	FDR
protein K11-linked ubiquitination	6	36.2×	2e-06
protein monoubiquitination	6	31.8×	3e-06
protein K48-linked ubiquitination	9	23.3×	5e-08
protein K63-linked ubiquitination	5	20.6×	3e-04
protein polyubiquitination	10	17.8×	5e-08
ubiquitin-dependent protein catabolic process	10	11.4×	2e-06

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	45
Likely pathogenic	23
Uncertain significance	148
Likely benign	138
Benign	58

Top pathogenic / likely-pathogenic (30)

Variant ID	HGVS	Classification
10805	NM_000381.4(MID1):c.1311GAT[1] (p.Met438del)	Pathogenic
10807	NM_000381.4(MID1):c.1558dup (p.Glu520fs)	Pathogenic
10808	NM_000381.4(MID1):c.1877T>C (p.Leu626Pro)	Pathogenic
10809	NM_000381.4(MID1):c.343G>T (p.Glu115Ter)	Pathogenic
10810	NG_008197.2:g.(218402_271087)_(271804_315503)dup	Pathogenic
10811	NM_000381.4(MID1):c.884T>C (p.Leu295Pro)	Pathogenic
10812	NM_000381.4(MID1):c.1546_1547del (p.Thr518_Pro519insTer)	Pathogenic
1210722	NM_000381.4(MID1):c.639_642del (p.Glu214fs)	Pathogenic
1299222	GRCh37/hg19 Xp22.2(chrX:10491132-10535643)x1	Pathogenic
1373272	NM_000381.4(MID1):c.971_978dup (p.Arg327fs)	Pathogenic
167301	NM_000381.4(MID1):c.1302_1305dup (p.Ser436Ter)	Pathogenic
1684290	NM_000381.4(MID1):c.673_674del (p.Glu224_Ser225insTer)	Pathogenic
1702864	NM_000381.4(MID1):c.1102C>T (p.Arg368Ter)	Pathogenic
1753481	NM_000381.4(MID1):c.1222G>T (p.Glu408Ter)	Pathogenic
198721	NM_000381.4(MID1):c.1444_1447dup (p.Ser483fs)	Pathogenic
2020625	NM_000381.4(MID1):c.669dup (p.Glu224fs)	Pathogenic
226291	GRCh37/hg19 Xp22.2(chrX:10299643-10638042)	Pathogenic
2422983	NC_000023.10:g.(?10450500)(10450688_?)del	Pathogenic
2422984	NC_000023.10:g.(?10491112)(10535587_?)del	Pathogenic
2422985	NC_000023.10:g.(?10417408)(10423137_?)del	Pathogenic
2572750	NM_000381.4(MID1):c.949del (p.Glu317fs)	Pathogenic
2754716	NM_000381.4(MID1):c.781A>T (p.Lys261Ter)	Pathogenic
2778832	NM_000381.4(MID1):c.202C>T (p.Arg68Ter)	Pathogenic
2809087	NM_000381.4(MID1):c.622C>T (p.Gln208Ter)	Pathogenic
29975	NM_000381.4(MID1):c.712G>T (p.Glu238Ter)	Pathogenic
3235986	NM_000381.4(MID1):c.671_674del (p.Glu224fs)	Pathogenic
3245800	NC_000023.10:g.(?10417408)(10463751_?)del	Pathogenic
3245811	NC_000023.10:g.(?10417408)(10427867_?)del	Pathogenic
3898633	NM_000381.4(MID1):c.865-2A>G	Pathogenic
4082029	NM_000381.4(MID1):c.1313_1316dup (p.Val440fs)	Pathogenic

SpliceAI

2464 predictions. Top by Δscore:

Variant	Effect	Δscore
X:10449714:TACC:T	acceptor_loss	1.0000
X:10449718:T:A	acceptor_loss	1.0000
X:10454864:GCTT:G	donor_loss	1.0000
X:10454865:CTTA:C	donor_loss	1.0000
X:10454866:TTAC:T	donor_loss	1.0000
X:10454867:TAC:T	donor_loss	1.0000
X:10454868:A:AC	donor_gain	1.0000
X:10454868:A:AT	donor_loss	1.0000
X:10454868:AC:A	donor_gain	1.0000
X:10454869:C:CC	donor_gain	1.0000
X:10454869:C:CT	donor_loss	1.0000
X:10454869:CC:C	donor_gain	1.0000
X:10454894:T:TA	donor_gain	1.0000
X:10454895:C:A	donor_gain	1.0000
X:10454939:C:CA	donor_gain	1.0000
X:10454948:C:A	donor_gain	1.0000
X:10455073:TTGGC:T	acceptor_gain	1.0000
X:10455074:TGGC:T	acceptor_gain	1.0000
X:10455075:GGC:G	acceptor_gain	1.0000
X:10455076:GC:G	acceptor_gain	1.0000
X:10455076:GCC:G	acceptor_loss	1.0000
X:10455077:CC:C	acceptor_gain	1.0000
X:10455078:C:CC	acceptor_gain	1.0000
X:10455085:CAAA:C	acceptor_gain	1.0000
X:10455086:A:T	acceptor_gain	1.0000
X:10455088:A:AC	acceptor_gain	1.0000
X:10455088:A:C	acceptor_gain	1.0000
X:10455091:C:CT	acceptor_gain	1.0000
X:10459639:CACT:C	donor_loss	1.0000
X:10459640:ACTT:A	donor_loss	1.0000

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000007843 (X:10626438 C>A,G,T), RS1000016389 (X:10667180 C>T), RS1000022228 (X:10600784 C>T), RS1000032110 (X:10600174 A>G,T), RS1000038743 (X:10679990 G>T), RS1000052243 (X:10510002 T>A,C), RS1000054737 (X:10746684 G>C), RS1000089703 (X:10774898 A>G), RS1000099684 (X:10778036 CT>C,CTT), RS1000109939 (X:10667637 G>A,T), RS1000131944 (X:10473223 A>G), RS1000138514 (X:10794644 A>G), RS1000151968 (X:10579153 G>C), RS1000158921 (X:10554302 A>G), RS1000186975 (X:10620664 G>C)

Disease associations

OMIM: gene MIM:300552 | disease phenotypes: MIM:300000, MIM:609296, MIM:220200

GenCC curated gene-disease

Disease	Classification	Inheritance
X-linked Opitz G/BBB syndrome	Definitive	X-linked

ClinGen Gene-Disease Validity (1)

Expert-panel classifications — Definitive > Strong > Moderate > Limited > Disputed > Refuted.

Disease	Classification	Inheritance
X-linked Opitz G/BBB syndrome	Definitive	XL

Mondo (3): X-linked Opitz G/BBB syndrome (MONDO:0010222), B-cell immunodeficiency, distal limb anomalies, and urogenital malformations (MONDO:0012243), Dandy-Walker syndrome (MONDO:0009072)

Orphanet (4): Opitz GBBB syndrome (Orphanet:2745), B-cell immunodeficiency-limb anomaly-urogenital malformation syndrome (Orphanet:567502), Isolated Dandy-Walker malformation (Orphanet:217), OBSOLETE: X-linked Opitz G/BBB syndrome (Orphanet:306597)

HPO phenotypes

96 total (30 of 96 shown, HPO-id order):

HPO	Term
HP:0000023	Inguinal hernia
HP:0000028	Cryptorchidism
HP:0000047	Hypospadias
HP:0000048	Bifid scrotum
HP:0000049	Shawl scrotum
HP:0000054	Micropenis
HP:0000076	Vesicoureteral reflux
HP:0000079	Abnormality of the urinary system
HP:0000119	Abnormality of the genitourinary system
HP:0000126	Hydronephrosis
HP:0000175	Cleft palate
HP:0000204	Cleft upper lip
HP:0000218	High palate
HP:0000219	Thin upper lip vermilion
HP:0000239	Large fontanelles
HP:0000252	Microcephaly
HP:0000260	Wide anterior fontanel
HP:0000316	Hypertelorism
HP:0000319	Smooth philtrum
HP:0000343	Long philtrum
HP:0000347	Micrognathia
HP:0000349	Widow’s peak
HP:0000358	Posteriorly rotated ears
HP:0000365	Hearing impairment
HP:0000369	Low-set ears
HP:0000431	Wide nasal bridge
HP:0000463	Anteverted nares
HP:0000486	Strabismus
HP:0000494	Downslanted palpebral fissures
HP:0000506	Telecanthus

GWAS associations

0 associations (top):

MeSH disease descriptors (2)

Descriptor	Name	Tree numbers
D003616	Dandy-Walker Syndrome	C10.228.140.252.300; C10.228.140.602.500; C10.500.205; C16.131.666.205
C563745	B-Cell Immunodeficiency, Distal Limb Anomalies, And Urogenital Malformations (supp.)

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

57 total (human), top 30 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects cotreatment, decreases expression, affects expression, increases expression	8
Benzo(a)pyrene	affects expression, affects methylation, decreases expression	5
Aflatoxin B1	decreases expression, decreases methylation	4
potassium chromate(VI)	decreases expression, affects cotreatment	2
Estradiol	increases expression, increases reaction, affects expression	2
Hydrogen Peroxide	increases expression, affects expression	2
Nickel	decreases expression	2
Phenylmercuric Acetate	affects cotreatment, decreases expression	2
Silicon Dioxide	decreases expression, increases expression	2
Tobacco Smoke Pollution	decreases expression, increases expression	2
7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide	affects expression, decreases expression	2
Cyclosporine	decreases expression	2
Cadmium Chloride	decreases expression, increases expression	2
Particulate Matter	decreases expression, increases abundance, affects cotreatment	2
FR900359	affects phosphorylation	1
sotorasib	affects cotreatment, decreases expression	1
methylmercuric chloride	decreases expression	1
trichostatin A	increases expression	1
arsenite	affects binding, decreases reaction	1
mono-(2-ethylhexyl)phthalate	decreases expression	1
tris(1,3-dichloro-2-propyl)phosphate	decreases expression	1
sodium arsenite	affects cotreatment, decreases expression, increases abundance	1
cobaltous chloride	decreases expression	1
manganese chloride	affects cotreatment, decreases expression, increases abundance	1
nickel sulfate	decreases expression	1
hydroquinone	decreases expression	1
diallyl trisulfide	decreases expression	1
epigallocatechin gallate	affects cotreatment, decreases expression, increases expression	1
chromium hexavalent ion	decreases expression	1
perfluorooctane sulfonic acid	decreases expression	1

Cellosaurus cell lines

3 cell lines: 3 cancer cell line

First 10 cell lines (id-ordered, not curated):

Cellosaurus	Name	Category	Sex
CVCL_E2CB	HAP1 MID1 (-) 1	Cancer cell line	Male
CVCL_E2CC	HAP1 MID1 (-) 2	Cancer cell line	Male
CVCL_E2CD	HAP1 MID1 (-) 3	Cancer cell line	Male

Clinical trials (associated diseases)

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