GEMIN7

gene
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Also known as FLJ13956

Summary

GEMIN7 (gem nuclear organelle associated protein 7, HGNC:20045) is a protein-coding gene on chromosome 19q13.32, encoding Gem-associated protein 7 (Q9H840). The SMN complex catalyzes the assembly of small nuclear ribonucleoproteins (snRNPs), the building blocks of the spliceosome, and thereby plays an important role in the splicing of cellular pre-mRNAs. It is a selective cancer dependency (DepMap: 84.9% of cell lines).

The protein encoded by this gene is a component of the core SMN complex, which is required for pre-mRNA splicing in the nucleus. The encoded protein is found in the nucleoplasm, in nuclear “gems” (Gemini of Cajal bodies), and in the cytoplasm. Three transcript variants encoding the same protein have been found for this gene.

Source: NCBI Gene 79760 — RefSeq curated summary.

At a glance

  • GWAS associations: 10
  • Clinical variants (ClinVar): 37 total
  • Druggable target: yes
  • Cancer dependency (DepMap): dependent in 84.9% of screened cell lines
  • MANE Select transcript: NM_024707

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:20045
Approved symbolGEMIN7
Namegem nuclear organelle associated protein 7
Location19q13.32
Locus typegene with protein product
StatusApproved
AliasesFLJ13956
Ensembl geneENSG00000142252
Ensembl biotypeprotein_coding
OMIM607419
Entrez79760

Gene structure

Transcript identifiers

Ensembl transcripts: 26 — 25 protein_coding, 1 protein_coding_CDS_not_defined

ENST00000270257, ENST00000391951, ENST00000591607, ENST00000591747, ENST00000592351, ENST00000885624, ENST00000885625, ENST00000885626, ENST00000885627, ENST00000885628, ENST00000885629, ENST00000885630, ENST00000885631, ENST00000885632, ENST00000885633, ENST00000925297, ENST00000925298, ENST00000925299, ENST00000925300, ENST00000925301, ENST00000925302, ENST00000925303, ENST00000925304, ENST00000925305, ENST00000956990, ENST00000956991

RefSeq mRNA: 5 — MANE Select: NM_024707 NM_001007269, NM_001007270, NM_001319054, NM_001319055, NM_024707

CCDS: CCDS12654

Canonical transcript exons

ENST00000270257 — 3 exons

ExonStartEnd
ENSE000009531304509010745091518
ENSE000010486564507990745080029
ENSE000029746464507926045079377

Expression profiles

Bgee: expression breadth ubiquitous, 214 present calls, max score 92.92.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 3.9815 / max 36.5861, expressed in 1435 samples.

FANTOM5 promoters (5 alternative TSS)

Promoter IDTPM avgSamples expressed
17638111.56521777
1763791.5750721
1763821.3334745
1763800.8565402
1763830.2167101

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
lower esophagus mucosaUBERON:003583492.92gold quality
mucosa of transverse colonUBERON:000499192.87gold quality
granulocyteCL:000009492.32gold quality
ileal mucosaUBERON:000033192.06gold quality
tibialis anteriorUBERON:000138591.50silver quality
monocyteCL:000057690.56gold quality
leukocyteCL:000073890.33gold quality
gastrocnemiusUBERON:000138889.84gold quality
hindlimb stylopod muscleUBERON:000425288.95gold quality
muscle of legUBERON:000138388.87gold quality
spleenUBERON:000210688.74gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047387.89gold quality
right lobe of liverUBERON:000111487.81gold quality
body of stomachUBERON:000116187.50gold quality
esophagus mucosaUBERON:000246987.49gold quality
skeletal muscle organUBERON:001489287.49gold quality
apex of heartUBERON:000209887.01gold quality
small intestine Peyer’s patchUBERON:000345486.33gold quality
transverse colonUBERON:000115786.28gold quality
adenohypophysisUBERON:000219686.27gold quality
skin of legUBERON:000151186.25gold quality
heart left ventricleUBERON:000208486.18gold quality
skin of abdomenUBERON:000141686.16gold quality
lymph nodeUBERON:000002985.86gold quality
cardiac ventricleUBERON:000208285.74gold quality
bloodUBERON:000017884.99gold quality
esophagusUBERON:000104384.88gold quality
right hemisphere of cerebellumUBERON:001489084.81gold quality
pituitary glandUBERON:000000784.74gold quality
vermiform appendixUBERON:000115484.67gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3yes10.19

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

28 targeting GEMIN7, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-6783-3P99.8967.922059
HSA-MIR-477999.8666.501583
HSA-MIR-430699.7270.503630
HSA-MIR-360999.5269.892587
HSA-MIR-548AH-5P99.5269.732626
HSA-MIR-392399.5269.21446
HSA-MIR-4677-3P99.4967.911246
HSA-MIR-185-5P99.3568.602497
HSA-MIR-464499.3569.122514
HSA-MIR-3160-5P99.2869.071938
HSA-MIR-4695-5P99.0664.871151
HSA-MIR-129498.9169.261030
HSA-MIR-998698.9169.281024
HSA-MIR-6868-3P98.6369.642259
HSA-MIR-374B-3P98.6368.241360
HSA-MIR-318898.5865.60878
HSA-MIR-426698.5367.291035
HSA-MIR-6730-5P98.0368.121299
HSA-MIR-5681A97.9967.171658
HSA-MIR-365297.7165.431890
HSA-MIR-66597.6065.641781
HSA-MIR-450B-3P97.5666.12512
HSA-MIR-443097.4765.611813
HSA-MIR-148B-5P97.2966.30992
HSA-MIR-6874-3P97.2966.34975
HSA-MIR-769-3P97.0664.83464
HSA-MIR-4793-5P96.8865.90872
HSA-MIR-770695.9663.68172

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 84.9% of screened cell lines.

Literature-anchored findings (GeneRIF, showing 3)

  • Identification and characterization a novel protein component of the survival of motor neurons complex termed Gemin7 using native purified SMN complexes and peptide sequencing by mass spectrometry (PMID:12065586)
  • Unrip is recruited to the active SMN complex via a stable interaction with Gemin7 (PMID:16159890)
  • Gemin8 has an essential role in the proper structural organization of the SMN complex and the involvement of the heteromeric subunit containing Gemin6, Gemin7, Gemin8, and Unrip in the recruitment of Sm proteins to the snRNP assembly pathway (PMID:17023415)

Cross-species orthologs

5 orthologs

OrganismSymbolGene ID
danio_reriogemin7ENSDARG00000041011
mus_musculusGemin7ENSMUSG00000044709
rattus_norvegicusGemin7l1ENSRNOG00000034168
rattus_norvegicusGemin7ENSRNOG00000049772
caenorhabditis_elegansWBGENE00007702

Protein

Protein identifiers

Gem-associated protein 7Q9H840 (reviewed: Q9H840)

Alternative names: SIP3

All UniProt accessions (1): Q9H840

UniProt curated annotations — full annotation on UniProt →

Function. The SMN complex catalyzes the assembly of small nuclear ribonucleoproteins (snRNPs), the building blocks of the spliceosome, and thereby plays an important role in the splicing of cellular pre-mRNAs. Most spliceosomal snRNPs contain a common set of Sm proteins SNRPB, SNRPD1, SNRPD2, SNRPD3, SNRPE, SNRPF and SNRPG that assemble in a heptameric protein ring on the Sm site of the small nuclear RNA to form the core snRNP (Sm core). In the cytosol, the Sm proteins SNRPD1, SNRPD2, SNRPE, SNRPF and SNRPG are trapped in an inactive 6S pICln-Sm complex by the chaperone CLNS1A that controls the assembly of the core snRNP. To assemble core snRNPs, the SMN complex accepts the trapped 5Sm proteins from CLNS1A forming an intermediate. Binding of snRNA inside 5Sm triggers eviction of the SMN complex, thereby allowing binding of SNRPD3 and SNRPB to complete assembly of the core snRNP.

Subunit / interactions. Part of the core SMN complex that contains SMN1, GEMIN2/SIP1, DDX20/GEMIN3, GEMIN4, GEMIN5, GEMIN6, GEMIN7, GEMIN8 and STRAP/UNRIP. Part of the SMN-Sm complex that contains SMN1, GEMIN2/SIP1, DDX20/GEMIN3, GEMIN4, GEMIN5, GEMIN6, GEMIN7, GEMIN8, STRAP/UNRIP and the Sm proteins SNRPB, SNRPD1, SNRPD2, SNRPD3, SNRPE, SNRPF and SNRPG. Interacts with GEMIN6; the interaction is direct. Interacts with STRAP/UNRIP; the interaction is direct. Interacts with GEMIN8; the interaction is direct. Interacts with SNRPB, SNRPD2, SNRPD3 and SNRPE; the interaction is direct.

Subcellular location. Nucleus. Nucleoplasm. Gem. Cytoplasm.

Similarity. Belongs to the gemin-7 family.

RefSeq proteins (5): NP_001007270, NP_001007271, NP_001305983, NP_001305984, NP_078983* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR020338SMN_gemin7Family
IPR024642SUZ-CDomain
IPR047575SmDomain

Pfam: PF11095

UniProt features (15 total): strand 6, helix 3, domain 2, modified residue 2, chain 1, turn 1

Structure

Experimental structures (PDB)

2 structures.

PDBMethodResolution (Å)
7BBLX-RAY DIFFRACTION1.52
1Y96X-RAY DIFFRACTION2

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q9H840-F180.430.57

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 (2): 1, 3

Function

Pathways and Gene Ontology

Reactome pathways

2 pathways

IDPathway
R-HSA-191859snRNP Assembly
R-HSA-9754678SARS-CoV-2 modulates host translation machinery

MSigDB gene sets: 114 (showing top): GSE45365_NK_CELL_VS_CD8A_DC_DN, MODULE_255, RORA1_01, ROVERSI_GLIOMA_COPY_NUMBER_UP, MODULE_317, TGACCTY_ERR1_Q2, GGGTGGRR_PAX4_03, MUELLER_PLURINET, KOYAMA_SEMA3B_TARGETS_UP, MODULE_480, GOBP_PROTEIN_RNA_COMPLEX_ORGANIZATION, GOBP_RNA_SPLICING, OCT1_06, GOBP_RIBONUCLEOPROTEIN_COMPLEX_BIOGENESIS, GOBP_SPLICEOSOMAL_SNRNP_ASSEMBLY

GO Biological Process (4): spliceosomal snRNP assembly (GO:0000387), mRNA splicing, via spliceosome (GO:0000398), mRNA processing (GO:0006397), RNA splicing (GO:0008380)

GO Molecular Function (2): RNA binding (GO:0003723), protein binding (GO:0005515)

GO Cellular Component (9): nucleoplasm (GO:0005654), cytoplasm (GO:0005737), cytosol (GO:0005829), nuclear body (GO:0016604), SMN complex (GO:0032797), SMN-Sm protein complex (GO:0034719), Gemini of Cajal bodies (GO:0097504), Sm-like protein family complex (GO:0120114), nucleus (GO:0005634)

Reactome top-level categories

Rollup of top-2 pathways:

CategoryPathways
Metabolism of non-coding RNA1
SARS-CoV-2-host interactions1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cellular anatomical structure3
RNA processing2
cytoplasm2
Sm-like protein family complex2
mRNA splicing, via spliceosome1
protein-RNA complex assembly1
RNA splicing, via transesterification reactions with bulged adenosine as nucleophile1
mRNA processing1
mRNA metabolic process1
nucleic acid binding1
binding1
nuclear lumen1
intracellular anatomical structure1
nucleoplasm1
intracellular membraneless organelle1
SMN-Sm protein complex1
SMN complex1
nuclear body1
protein-containing complex1
intracellular membrane-bounded organelle1

Protein interactions and networks

STRING

698 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
GEMIN7GEMIN2O14893993
GEMIN7GEMIN6Q8WXD5993
GEMIN7STRAPQ9Y3F4974
GEMIN7GEMIN8Q9NWZ8968
GEMIN7DDX20Q9UHI6943
GEMIN7GEMIN5Q8TEQ6937
GEMIN7GEMIN4P57678881
GEMIN7CSDE1O75534782
GEMIN7SNRPEP08578682
GEMIN7SMN1Q16637675
GEMIN7SNRPBP14678584
GEMIN7HNRNPRO43390561
GEMIN7PHAXQ9H814548
GEMIN7SNRPD3P43331534
GEMIN7COILP38432533

IntAct

81 interactions, top by confidence:

ABTypeScore
GEMIN6GEMIN7psi-mi:“MI:0915”(physical association)0.960
GEMIN7GEMIN6psi-mi:“MI:0915”(physical association)0.960
GEMIN6GEMIN7psi-mi:“MI:0407”(direct interaction)0.960
SMN1GEMIN2psi-mi:“MI:0914”(association)0.960
SNRPFGEMIN2psi-mi:“MI:0914”(association)0.910
STK24STRNpsi-mi:“MI:0914”(association)0.870
SNRPEGEMIN2psi-mi:“MI:0914”(association)0.770
GEMIN7STRAPpsi-mi:“MI:0407”(direct interaction)0.760
STRAPGEMIN7psi-mi:“MI:0407”(direct interaction)0.760
GEMIN7SNRNP70psi-mi:“MI:0914”(association)0.730
GEMIN4SNRNP70psi-mi:“MI:0914”(association)0.730
NCKIPSDGEMIN2psi-mi:“MI:0914”(association)0.640
SNRNP70GEMIN2psi-mi:“MI:0914”(association)0.640
STRAPCDK2AP1psi-mi:“MI:0914”(association)0.530
DDX20GAPDHSpsi-mi:“MI:0914”(association)0.530
SNRNP70GTPBP1psi-mi:“MI:0914”(association)0.530
SNRPEPRMT5psi-mi:“MI:0914”(association)0.530
GEMIN7GEMIN2psi-mi:“MI:0914”(association)0.530

BioGRID (118): GEMIN6 (Two-hybrid), GEMIN6 (Two-hybrid), GEMIN6 (Two-hybrid), CSNK1D (Affinity Capture-MS), EZH2 (Affinity Capture-MS), ITGB4 (Affinity Capture-MS), SMN1 (Affinity Capture-MS), SNRNP70 (Affinity Capture-MS), SNRPD1 (Affinity Capture-MS), GEMIN2 (Affinity Capture-MS), FARP1 (Affinity Capture-MS), RCL1 (Affinity Capture-MS), YME1L1 (Affinity Capture-MS), STRAP (Affinity Capture-MS), DDX20 (Affinity Capture-MS)

ESM2 similar proteins: A2BIG9, A4IGZ4, B0R0W9, B4H303, B7PXE3, D3ZEY4, G2TRR1, H9JD76, O15116, O74499, O75912, P0C550, P23059, P32019, P33279, P47017, P53905, P87173, Q03606, Q0JKV1, Q17QA0, Q17QV9, Q4R8E0, Q52T38, Q58DC8, Q5E9Z8, Q5ZK92, Q6AZT2, Q6GQ67, Q6NU60, Q6NW58, Q6P5D3, Q8IPZ7, Q8K337, Q8LFL8, Q8VC85, Q945P8, Q96P47, Q96S15, Q9BRA0

Diamond homologs: Q17QA0, Q9CWY4, Q9H840, G2TRR1

SIGNOR signaling

1 interactions.

AEffectBMechanism
GEMIN7“form complex”“SMN complex”binding

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 69 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:

PathwayPartnersFoldFDR
Metabolism of non-coding RNA564.7×1e-06
snRNP Assembly1251.8×1e-15
SARS-CoV-2 modulates host translation machinery1045.7×2e-12
Metabolism of RNA76.0×7e-03

GO biological processes:

GO termPartnersFoldFDR
spliceosomal snRNP assembly13121.8×2e-22
spliceosomal complex assembly548.5×1e-05
mRNA splicing, via spliceosome68.9×7e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance29
Likely benign2
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

517 predictions. Top by Δscore:

VariantEffectΔscore
19:45075711:A:ACdonor_gain1.0000
19:45075711:AC:Adonor_gain1.0000
19:45075711:ACC:Adonor_loss1.0000
19:45075712:C:CCdonor_gain1.0000
19:45075712:CC:Cdonor_gain1.0000
19:45075712:CCT:Cdonor_gain1.0000
19:45075712:CCTG:Cdonor_gain1.0000
19:45075859:CGGT:Cacceptor_gain1.0000
19:45075860:GGT:Gacceptor_gain1.0000
19:45075861:GT:Gacceptor_gain1.0000
19:45075862:TCT:Tacceptor_loss1.0000
19:45075863:C:CCacceptor_gain1.0000
19:45075863:CTGCA:Cacceptor_loss1.0000
19:45090098:A:AGacceptor_gain1.0000
19:45090099:C:Gacceptor_gain1.0000
19:45090102:A:AGacceptor_gain1.0000
19:45090105:A:AGacceptor_gain1.0000
19:45090105:A:ATacceptor_loss1.0000
19:45090106:G:GGacceptor_gain1.0000
19:45090106:GC:Gacceptor_gain1.0000
19:45090106:GCC:Gacceptor_gain1.0000
19:45090106:GCCA:Gacceptor_gain1.0000
19:45090106:GCCAA:Gacceptor_gain1.0000
19:45075708:CTCA:Cdonor_gain0.9900
19:45075712:CCTGA:Cdonor_gain0.9900
19:45075858:GCGGT:Gacceptor_gain0.9900
19:45075859:CGGTC:Cacceptor_gain0.9900
19:45075861:GTCT:Gacceptor_gain0.9900
19:45075862:TCTGC:Tacceptor_gain0.9900
19:45075866:C:CTacceptor_gain0.9900

AlphaMissense

830 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
19:45090353:T:CF80S0.994
19:45090470:T:AL119H0.991
19:45090319:A:CS69R0.989
19:45090321:C:AS69R0.989
19:45090321:C:GS69R0.989
19:45090434:T:CL107P0.989
19:45090419:T:CF102S0.988
19:45090187:T:CF25L0.986
19:45090189:T:AF25L0.986
19:45090189:T:GF25L0.986
19:45090310:T:GY66D0.986
19:45090425:T:AV104E0.985
19:45090463:G:CA117P0.985
19:45090482:A:TD123V0.985
19:45090314:T:CL67P0.983
19:45090493:T:GY127D0.982
19:45090434:T:AL107Q0.981
19:45090389:T:CF92S0.980
19:45090449:G:AG112D0.976
19:45090470:T:CL119P0.975
19:45090482:A:CD123A0.975
19:45090481:G:CD123H0.974
19:45090483:C:AD123E0.974
19:45090483:C:GD123E0.974
19:45090383:C:AA90D0.973
19:45090464:C:AA117E0.973
19:45090482:A:GD123G0.973
19:45090470:T:GL119R0.972
19:45090473:G:CR120P0.972
19:45090311:A:CY66S0.971

dbSNP variants (sampled 300 via entrez): RS1000032922 (19:45073654 G>A), RS1000132736 (19:45079173 A>G), RS1000141476 (19:45077508 G>T), RS1000363910 (19:45083598 T>C), RS1000545230 (19:45083060 T>C,G), RS1000612333 (19:45089514 G>C), RS1000646217 (19:45083762 G>A), RS1000657357 (19:45078132 A>C,G), RS1000740619 (19:45084118 C>G,T), RS1001351208 (19:45078797 G>A), RS1001430582 (19:45074869 G>A,C), RS1001540621 (19:45078370 G>A,C), RS1001589249 (19:45086482 A>G), RS1001634573 (19:45089009 T>G), RS1001832017 (19:45083318 G>A)

Disease associations

OMIM: gene MIM:607419 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

10 associations (top):

StudyTraitp-value
GCST004069_16Cerebrospinal fluid AB1-42 levels6.000000e-10
GCST005950_15Body mass index x sex x age interaction (4df test)2.000000e-10
GCST005951_56Body mass index1.000000e-06
GCST005952_8Body mass index (age>50)9.000000e-12
GCST005954_4Body mass index x age interaction2.000000e-07
GCST007320_89Alzheimer’s disease or family history of Alzheimer’s disease1.000000e-08
GCST007827_13Alzheimer’s disease or HDL levels (pleiotropy)7.000000e-22
GCST007827_3Alzheimer’s disease or HDL levels (pleiotropy)1.000000e-97
GCST007827_5Alzheimer’s disease or HDL levels (pleiotropy)7.000000e-74
GCST007827_8Alzheimer’s disease or HDL levels (pleiotropy)3.000000e-36

EFO canonical traits (6, from GWAS)

EFO IDTrait name
EFO:0004670beta-amyloid 1-42 measurement
EFO:0004340body mass index
EFO:0008007age at assessment
EFO:0008343sex interaction measurement
EFO:0009268family history of Alzheimer’s disease
EFO:0004612high density lipoprotein cholesterol measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL4105841 (SINGLE PROTEIN)

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

CTD chemical–gene interactions

21 total (human), top 21 by PubMed support.

ChemicalActions (top 5)PubMed papers
GSK-J4decreases expression1
FR900359increases phosphorylation1
sodium arsenitedecreases expression1
di-n-butylphosphoric acidaffects expression1
CGP 52608affects binding, increases reaction1
Grape Seed Proanthocyanidinsaffects cotreatment, decreases expression1
Resveratrolaffects cotreatment, increases expression1
Leflunomidedecreases expression1
Benzo(a)pyrenedecreases methylation1
Catechinaffects cotreatment, decreases expression1
Ethyl Methanesulfonatedecreases expression1
Gallic Aciddecreases expression1
Ivermectindecreases expression1
Methyl Methanesulfonatedecreases expression1
Plant Extractsaffects cotreatment, increases expression1
Smokedecreases expression1
Tobacco Smoke Pollutiondecreases expression1
Valproic Acidincreases expression1
Cadmium Chloridedecreases expression1
Copper Sulfatedecreases expression1
Lactic Aciddecreases expression1

ChEMBL screening assays

1 unique, capped per target: 1 binding

Representative assays (with source publication via chembl_document):

Assay IDTypeDescriptionSource paper
CHEMBL4012567BindingBinding affinity to GEMIN7 in human INA-6 cells after 3 hrs by nanoLC-MS/MS methodUgi Reaction-Derived α-Acyl Aminocarboxamides Bind to Phosphatidylinositol 3-Kinase-Related Kinases, Inhibit HSF1-Dependent Heat Shock Response, and Induce Apoptosis in Multiple Myeloma Cells. — J Med Chem

Clinical trials (associated diseases)

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

No linked Atlas pages yet — the cross-entity mesh grows as the corpus expands.