EMID1

Summary

EMID1 (EMI domain containing 1, HGNC:18036) is a protein-coding gene on chromosome 22q12.2, encoding EMI domain-containing protein 1 (Q96A84).

Predicted to be located in several cellular components, including Golgi apparatus; endoplasmic reticulum; and extracellular matrix. Predicted to be part of collagen trimer.

Source: NCBI Gene 129080 — RefSeq curated summary.

At a glance

• GWAS associations: 24
• Clinical variants (ClinVar): 99 total
• MANE Select transcript: NM_133455

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:18036
Approved symbol	EMID1
Name	EMI domain containing 1
Location	22q12.2
Locus type	gene with protein product
Status	Approved
Aliases	EMU1, hEmu1, EMI5
Ensembl gene	ENSG00000186998
Ensembl biotype	protein_coding
OMIM	608926
Entrez	129080

Gene structure

Transcript identifiers

Ensembl transcripts: 22 — 17 protein_coding, 3 retained_intron, 1 nonsense_mediated_decay, 1 protein_coding_CDS_not_defined

ENST00000334018, ENST00000404755, ENST00000404820, ENST00000429226, ENST00000430127, ENST00000433143, ENST00000435427, ENST00000473933, ENST00000484039, ENST00000487477, ENST00000488820, ENST00000891447, ENST00000891448, ENST00000891449, ENST00000891450, ENST00000935681, ENST00000935682, ENST00000935683, ENST00000961472, ENST00000961473, ENST00000961474, ENST00000961475

RefSeq mRNA: 3 — MANE Select: NM_133455 NM_001267895, NM_001410828, NM_133455

CCDS: CCDS33630, CCDS93143

Canonical transcript exons

ENST00000334018 — 15 exons

Exon	Start	End
ENSE00001611508	29226490	29226551
ENSE00001670727	29215527	29215630
ENSE00001695101	29214926	29215039
ENSE00001754790	29258817	29259597
ENSE00001913306	29205896	29206139
ENSE00003505907	29231020	29231140
ENSE00003509919	29232256	29232402
ENSE00003514554	29233614	29233666
ENSE00003560263	29233379	29233468
ENSE00003562725	29231593	29231682
ENSE00003581986	29225133	29225216
ENSE00003645065	29234137	29234199
ENSE00003662632	29234305	29234349
ENSE00003683197	29254203	29254287
ENSE00003786137	29243445	29243489

Expression profiles

Bgee: expression breadth ubiquitous, 192 present calls, max score 92.96.

FANTOM5 (CAGE): breadth broad, TPM avg 4.3481 / max 403.3496, expressed in 740 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
191595	4.1542	736
191596	0.1939	110

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
ventricular zone	UBERON:0003053	92.96	gold quality
spleen	UBERON:0002106	92.34	gold quality
right adrenal gland cortex	UBERON:0035827	90.09	gold quality
right adrenal gland	UBERON:0001233	89.85	gold quality
cortical plate	UBERON:0005343	89.60	gold quality
left adrenal gland cortex	UBERON:0035825	89.31	gold quality
left adrenal gland	UBERON:0001234	89.21	gold quality
amygdala	UBERON:0001876	88.81	gold quality
adrenal cortex	UBERON:0001235	88.53	gold quality
cingulate cortex	UBERON:0003027	88.36	gold quality
anterior cingulate cortex	UBERON:0009835	88.26	gold quality
ganglionic eminence	UBERON:0004023	88.02	gold quality
adrenal gland	UBERON:0002369	87.32	gold quality
right frontal lobe	UBERON:0002810	87.30	gold quality
temporal lobe	UBERON:0001871	86.37	gold quality
nucleus accumbens	UBERON:0001882	86.37	gold quality
caudate nucleus	UBERON:0001873	86.33	gold quality
prefrontal cortex	UBERON:0000451	86.05	gold quality
neocortex	UBERON:0001950	85.94	gold quality
frontal cortex	UBERON:0001870	85.32	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	85.22	gold quality
cerebral cortex	UBERON:0000956	85.05	gold quality
telencephalon	UBERON:0001893	84.92	gold quality
putamen	UBERON:0001874	84.89	gold quality
Brodmann (1909) area 9	UBERON:0013540	84.59	gold quality
Ammon’s horn	UBERON:0001954	84.17	gold quality
entorhinal cortex	UBERON:0002728	83.88	gold quality
forebrain	UBERON:0001890	82.71	gold quality
Brodmann (1909) area 46	UBERON:0006483	82.57	silver quality
embryo	UBERON:0000922	82.34	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-HCAD-10	yes	18.70
E-ANND-3	yes	4.85
E-MTAB-8060	no	226.76

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

14 targeting EMID1, 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-4779	99.86	66.50	1583
HSA-MIR-4728-5P	99.85	69.39	4718
HSA-MIR-6785-5P	99.82	68.68	4428
HSA-MIR-149-3P	99.72	68.22	3963
HSA-MIR-6883-5P	99.69	68.05	3785
HSA-MIR-5004-5P	99.68	66.63	1294
HSA-MIR-4649-3P	99.56	66.90	1783
HSA-MIR-4667-3P	99.26	65.45	1608
HSA-MIR-6773-3P	98.17	65.51	1213
HSA-MIR-6847-5P	97.93	66.74	1808
HSA-MIR-4638-3P	97.90	65.75	905
HSA-MIR-3085-5P	97.72	65.43	544
HSA-MIR-6793-3P	97.66	65.78	1084
HSA-MIR-5195-5P	90.84	65.09	287

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Emid1	ENSMUSG00000034164
rattus_norvegicus	Emid1	ENSRNOG00000033575

Paralogs (37): COL9A2 (ENSG00000049089), COL23A1 (ENSG00000050767), COL11A1 (ENSG00000060718), COL17A1 (ENSG00000065618), COL5A3 (ENSG00000080573), COL4A4 (ENSG00000081052), COL16A1 (ENSG00000084636), COL9A3 (ENSG00000092758), COL20A1 (ENSG00000101203), COL1A1 (ENSG00000108821), COL9A1 (ENSG00000112280), COL7A1 (ENSG00000114270), COL21A1 (ENSG00000124749), COL5A1 (ENSG00000130635), COL4A2 (ENSG00000134871), COL2A1 (ENSG00000139219), COL6A1 (ENSG00000142156), COL6A2 (ENSG00000142173), EDA (ENSG00000158813), COL26A1 (ENSG00000160963), COL1A2 (ENSG00000164692), COL3A1 (ENSG00000168542), COL4A3 (ENSG00000169031), COL22A1 (ENSG00000169436), COL24A1 (ENSG00000171502), COL18A1 (ENSG00000182871), COL4A1 (ENSG00000187498), COL4A5 (ENSG00000188153), COL25A1 (ENSG00000188517), COL27A1 (ENSG00000196739), COL13A1 (ENSG00000197467), COL4A6 (ENSG00000197565), COL11A2 (ENSG00000204248), COL5A2 (ENSG00000204262), COL15A1 (ENSG00000204291), COLQ (ENSG00000206561), COL28A1 (ENSG00000215018)

Protein

Protein identifiers

EMI domain-containing protein 1 — Q96A84 (reviewed: Q96A84)

Alternative names: Emilin and multimerin domain-containing protein 1

All UniProt accessions (7): B0QYK2, B0QYK3, B0QYK4, B0QYK5, F8WDX7, H0Y6W4, Q96A84

UniProt curated annotations — full annotation on UniProt →

Subunit / interactions. Homo- or heteromers.

Subcellular location. Secreted. Extracellular space. Extracellular matrix.

Post-translational modifications. O-fucosylated at Thr-42 within the EMI domain by POFUT3 and POFUT4.

Miscellaneous. May be due to a competing acceptor splice site. May be due to a competing acceptor splice site.

Isoforms (3)

UniProt ID	Names	Canonical?
Q96A84-1	1	yes
Q96A84-2	2
Q96A84-3	3

RefSeq proteins (3): NP_001254824, NP_001397757, NP_597712* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR008160	Collagen	Repeat
IPR011489	EMI_domain	Domain
IPR050392	Collagen/C1q_domain	Family

Pfam: PF01391, PF07546

UniProt features (23 total): compositionally biased region 8, glycosylation site 3, disulfide bond 3, domain 2, splice variant 2, region of interest 2, signal peptide 1, chain 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q96A84-F1	51.77	0.00

Functional residue map

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

Disulfide bonds (3): 37–96, 62–68, 95–104

Glycosylation sites (3): 42, 51, 136

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

ID	Pathway
R-HSA-5173105	O-linked glycosylation

MSigDB gene sets: 120 (showing top): GOCC_COLLAGEN_TRIMER, GGGTGGRR_PAX4_03, NKX62_Q2, MODULE_379, BLALOCK_ALZHEIMERS_DISEASE_UP, TGGNNNNNNKCCAR_UNKNOWN, HAND1E47_01, ZHANG_BREAST_CANCER_PROGENITORS_UP, MODULE_242, YYCATTCAWW_UNKNOWN, YAGI_AML_WITH_11Q23_REARRANGED, MODULE_104, GOCC_ENDOPLASMIC_RETICULUM_LUMEN, GAUSSMANN_MLL_AF4_FUSION_TARGETS_G_UP, MODULE_13

GO Biological Process (0):

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

GO Cellular Component (6): collagen trimer (GO:0005581), endoplasmic reticulum lumen (GO:0005788), Golgi apparatus (GO:0005794), extracellular matrix (GO:0031012), extracellular region (GO:0005576), endoplasmic reticulum (GO:0005783)

Reactome top-level categories

Rollup of top-1 pathways:

Category	Pathways
Post-translational protein modification	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cytoplasm	2
endomembrane system	2
intracellular membrane-bounded organelle	2
binding	1
protein-containing complex	1
endoplasmic reticulum	1
intracellular organelle lumen	1
external encapsulating structure	1
cellular anatomical structure	1

Protein interactions and networks

STRING

654 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
EMID1	SERPINH1	P29043	833
EMID1	THOC2	Q8NI27	565
EMID1	CD164L2	Q6UWJ8	447
EMID1	MRPL45	Q9BRJ2	441
EMID1	MMRN2	Q9H8L6	441
EMID1	EMILIN3	Q9NT22	411
EMID1	CCER2	I3L3R5	405
EMID1	OR51D1	Q8NGF3	380
EMID1	ZMAT5	Q9UDW3	380
EMID1	VPREB1	P12018	374
EMID1	TEX38	Q6PEX7	368
EMID1	SERTAD3	Q9UJW9	367
EMID1	POFUT2	Q9Y2G5	363
EMID1	MYPOP	Q86VE0	349
EMID1	UBE2QL1	A1L167	338

IntAct

10 interactions, top by confidence:

A	B	Type	Score
AKTIP	EMID1	psi-mi:“MI:0915”(physical association)	0.370
EMID1	CDC5L	psi-mi:“MI:0915”(physical association)	0.370
KRT40	ANKRD36	psi-mi:“MI:0914”(association)	0.350
EMID1	CRTAP	psi-mi:“MI:0914”(association)	0.350
EMID1	POTEF	psi-mi:“MI:0914”(association)	0.350
KRT40	NEURL1B	psi-mi:“MI:0914”(association)	0.350
NPTXR	ACACB	psi-mi:“MI:0914”(association)	0.350
EMID1	NDUFS4	psi-mi:“MI:0914”(association)	0.350
	EMID1	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (40): KLHL25 (Affinity Capture-MS), UBR4 (Affinity Capture-MS), COLGALT2 (Affinity Capture-MS), YTHDF1 (Affinity Capture-MS), EMID1 (Synthetic Lethality), KLHL25 (Affinity Capture-MS), YTHDF1 (Affinity Capture-MS), CRTAP (Affinity Capture-MS), EMID1 (Affinity Capture-RNA), YTHDF1 (Affinity Capture-MS), P3H1 (Affinity Capture-MS), EMID1 (Affinity Capture-MS), CRTAP (Affinity Capture-MS), KLHL25 (Affinity Capture-MS), SDF2L1 (Affinity Capture-MS)

ESM2 similar proteins: A1XQX1, A6NFA1, B1ATG9, C0HL12, O09010, O12971, O12972, O15399, O54693, O75973, O88992, P48807, P52795, P52796, P98172, Q03391, Q13563, Q20FD0, Q28143, Q3UHD1, Q4GZT3, Q4ZJM9, Q5FVH0, Q5QQ50, Q5QQ51, Q5VWW1, Q62645, Q6NW40, Q6PFE7, Q6ZRP7, Q7TQ33, Q7Z5L3, Q86V40, Q86Z23, Q8CFR0, Q8IYR6, Q8IZP7, Q8K479, Q924T4, Q92838

Diamond homologs: A6H6E2, F1QC17, P59900, Q13201, Q8K482, Q91VF6, Q96A83, Q96A84, Q99K41, Q9BXX0, Q9H8L6, Q9NT22, Q9Y6C2, B2RPV6, Q5RJ80, Q8BVD7, Q91VF5, Q9BXJ2, Q9W332, Q05A80, Q6IMN6, Q8R066, Q9BXJ3, P83425, Q4ZJM7, Q5FVH0, Q8K479, Q9BXJ0, P27658, Q7Z5L3, Q8CFR0, A6NHN0, Q0II24

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	71
Likely benign	2
Benign	1

Top pathogenic / likely-pathogenic (0)

SpliceAI

3155 predictions. Top by Δscore:

Variant	Effect	Δscore
22:29231016:TCA:T	acceptor_loss	1.0000
22:29231018:A:AG	acceptor_gain	1.0000
22:29231018:AGAT:A	acceptor_gain	1.0000
22:29231018:AGATG:A	acceptor_loss	1.0000
22:29231019:G:GC	acceptor_gain	1.0000
22:29231019:GA:G	acceptor_gain	1.0000
22:29231019:GAT:G	acceptor_gain	1.0000
22:29231019:GATG:G	acceptor_gain	1.0000
22:29231137:CAGGG:C	donor_loss	1.0000
22:29231138:AGGGT:A	donor_loss	1.0000
22:29231139:GG:G	donor_gain	1.0000
22:29231140:GG:G	donor_gain	1.0000
22:29231140:GGT:G	donor_loss	1.0000
22:29231141:G:GG	donor_gain	1.0000
22:29231141:GTG:G	donor_loss	1.0000
22:29231380:G:GT	donor_gain	1.0000
22:29231591:A:AG	acceptor_gain	1.0000
22:29231592:G:GG	acceptor_gain	1.0000
22:29233467:GG:G	donor_gain	1.0000
22:29233468:GG:G	donor_gain	1.0000
22:29233468:GGTA:G	donor_loss	1.0000
22:29233469:G:GG	donor_gain	1.0000
22:29233469:G:T	donor_loss	1.0000
22:29233470:TAA:T	donor_loss	1.0000
22:29233474:T:G	donor_gain	1.0000
22:29233667:G:GG	donor_gain	1.0000
22:29234196:GAGA:G	donor_gain	1.0000
22:29234198:GA:G	donor_gain	1.0000
22:29234200:G:GG	donor_gain	1.0000
22:29234301:A:AG	acceptor_gain	1.0000

AlphaMissense

2800 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000000982 (22:29235993 T>C), RS1000050567 (22:29252404 T>C,G), RS1000054484 (22:29244627 A>G), RS1000109706 (22:29244870 CT>C), RS1000110682 (22:29242977 T>C), RS1000290174 (22:29224399 T>G), RS1000297295 (22:29215911 A>G), RS1000304987 (22:29221209 C>T), RS1000384261 (22:29229902 T>C), RS1000425545 (22:29224260 G>A), RS1000469011 (22:29215744 G>A,C), RS1000530894 (22:29247527 T>C), RS1000558132 (22:29240994 G>C), RS1000560722 (22:29204617 T>C), RS1000584818 (22:29219753 G>C)

Disease associations

OMIM: gene MIM:608926 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

24 associations (top):

Study	Trait	p-value
GCST001937_28	Breast cancer	3.000000e-09
GCST002553_2	Pancreatic cancer	1.000000e-08
GCST004611_168	High light scatter reticulocyte count	7.000000e-13
GCST004612_189	High light scatter reticulocyte percentage of red cells	3.000000e-12
GCST004619_18	Reticulocyte fraction of red cells	1.000000e-10
GCST004622_95	Reticulocyte count	5.000000e-11
GCST004625_196	Monocyte count	5.000000e-10
GCST005580_24	Intraocular pressure	3.000000e-14
GCST006394_62	Intraocular pressure	5.000000e-17
GCST006412_131	Intraocular pressure	6.000000e-16
GCST006479_20	Diverticular disease	8.000000e-06
GCST009725_15	Intraocular pressure	2.000000e-17
GCST011742_70	Triglyceride levels in HIV infection	6.000000e-06
GCST90002385_575	High light scatter reticulocyte count	5.000000e-26
GCST90002386_530	High light scatter reticulocyte percentage of red cells	1.000000e-24
GCST90002388_266	Lymphocyte count	2.000000e-17
GCST90002393_588	Monocyte count	2.000000e-22
GCST90002397_595	Mean spheric corpuscular volume	2.000000e-10
GCST90002398_26	Neutrophil count	2.000000e-12
GCST90002400_504	Plateletcrit	2.000000e-15
GCST90002402_643	Platelet count	1.000000e-17
GCST90002405_412	Reticulocyte count	3.000000e-24
GCST90002406_565	Reticulocyte fraction of red cells	9.000000e-23
GCST90002407_195	White blood cell count	6.000000e-19

EFO canonical traits (9, from GWAS)

EFO ID	Trait name
EFO:0007986	reticulocyte count
EFO:0005091	monocyte count
EFO:0004695	intraocular pressure measurement
EFO:0009959	diverticular disease
EFO:0004530	triglyceride measurement
EFO:0004587	lymphocyte count
EFO:0004833	neutrophil count
EFO:0007985	platelet crit
EFO:0004309	platelet count

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

18 total (human), top 18 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Benzo(a)pyrene	affects methylation, increases methylation	2
methylmercuric chloride	decreases expression	1
aflatoxin B2	increases methylation	1
CGP 52608	affects binding, increases reaction	1
abrine	decreases expression	1
2,3,5-trichloro-6-phenyl-(1,4)benzoquinone	decreases expression	1
Sunitinib	decreases expression	1
Ethanol	increases expression	1
Silicon Dioxide	decreases expression	1
Tobacco Smoke Pollution	decreases expression	1
Tretinoin	decreases expression	1
Triclosan	increases expression	1
Urethane	decreases expression	1
Valproic Acid	decreases expression, increases methylation	1
Zinc	increases expression	1
Antirheumatic Agents	decreases expression	1
Zinc Sulfate	increases expression	1
Acrylamide	increases expression	1

Clinical trials (associated diseases)

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