EFTUD2

gene
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Also known as U5-116KDSnrp116Snu114SNRNP116

Summary

EFTUD2 (elongation factor Tu GTP binding domain containing 2, HGNC:30858) is a protein-coding gene on chromosome 17q21.31, encoding 116 kDa U5 small nuclear ribonucleoprotein component (Q15029). Required for pre-mRNA splicing as component of the spliceosome, including pre-catalytic, catalytic and post-catalytic spliceosomal complexes. It is a common-essential gene (DepMap: required in 99.8% of cancer cell lines) and haploinsufficient (ClinGen: sufficient evidence).

This gene encodes a GTPase which is a component of the spliceosome complex which processes precursor mRNAs to produce mature mRNAs. Mutations in this gene are associated with mandibulofacial dysostosis with microcephaly. Multiple transcript variants encoding different isoforms have been found for this gene.

Source: NCBI Gene 9343 — RefSeq curated summary.

At a glance

  • Gene–disease (curated): mandibulofacial dysostosis-microcephaly syndrome (Definitive, ClinGen)
  • GWAS associations: 2
  • Clinical variants (ClinVar): 956 total — 99 pathogenic, 70 likely-pathogenic
  • Phenotypes (HPO): 46
  • Druggable target: yes — 1 molecules with ChEMBL bioactivity
  • Cancer driver (intOGen): activating (oncogene-like) across 1 cancer types
  • Cancer dependency (DepMap): dependent in 99.8% of screened cell lines (common-essential)
  • Dosage sensitivity (ClinGen): haploinsufficiency sufficient evidence, triplosensitivity no evidence
  • MANE Select transcript: NM_004247

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:30858
Approved symbolEFTUD2
Nameelongation factor Tu GTP binding domain containing 2
Location17q21.31
Locus typegene with protein product
StatusApproved
AliasesU5-116KD, Snrp116, Snu114, SNRNP116
Ensembl geneENSG00000108883
Ensembl biotypeprotein_coding
OMIM603892
Entrez9343

Gene structure

Transcript identifiers

Ensembl transcripts: 42 — 23 protein_coding, 14 retained_intron, 3 nonsense_mediated_decay, 2 protein_coding_CDS_not_defined

ENST00000402521, ENST00000426333, ENST00000585616, ENST00000585794, ENST00000586276, ENST00000586654, ENST00000586875, ENST00000587914, ENST00000587957, ENST00000588340, ENST00000588374, ENST00000589211, ENST00000589475, ENST00000589769, ENST00000589825, ENST00000590105, ENST00000590124, ENST00000590367, ENST00000590977, ENST00000591382, ENST00000591856, ENST00000592408, ENST00000592576, ENST00000592701, ENST00000593072, ENST00000593200, ENST00000880573, ENST00000880574, ENST00000880575, ENST00000880576, ENST00000880577, ENST00000925102, ENST00000925103, ENST00000925104, ENST00000925105, ENST00000969863, ENST00000969864, ENST00000969865, ENST00000969866, ENST00000969867, ENST00000969868, ENST00000969869

RefSeq mRNA: 4 — MANE Select: NM_004247 NM_001142605, NM_001258353, NM_001258354, NM_004247

CCDS: CCDS11489, CCDS45707, CCDS59295

Canonical transcript exons

ENST00000426333 — 28 exons

ExonStartEnd
ENSE000007317104487593444876100
ENSE000007317124487244644872570
ENSE000008979944485351744853635
ENSE000008979964485426944854356
ENSE000015628014484994844851369
ENSE000027539404489936944899445
ENSE000034695314485171044851817
ENSE000034853244485491844855004
ENSE000035050084488168744881722
ENSE000035200404488309344883158
ENSE000035359564485240944852562
ENSE000035409604485990544860045
ENSE000035428764486271344862906
ENSE000035434144486828744868350
ENSE000035529704487955644879638
ENSE000035733854489441744894525
ENSE000035841544486365544863782
ENSE000035845664485329644853390
ENSE000036278664485455644854682
ENSE000036335434486780744867897
ENSE000036390724485707544857157
ENSE000036444924488525644885334
ENSE000036547034486493044865065
ENSE000036574824488364944883724
ENSE000036588034488055444880644
ENSE000036702104486043244860543
ENSE000036875954485908044859181
ENSE000037561204488658544886750

Expression profiles

Bgee: expression breadth ubiquitous, 253 present calls, max score 97.07.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 48.0302 / max 1019.3506, expressed in 1823 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter IDTPM avgSamples expressed
16640347.01141823
1664041.0188516

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
bone marrow cellCL:000209297.07gold quality
tibialis anteriorUBERON:000138596.82gold quality
ventricular zoneUBERON:000305396.81gold quality
adrenal tissueUBERON:001830396.72gold quality
monocyteCL:000057696.68gold quality
leukocyteCL:000073896.61gold quality
ileal mucosaUBERON:000033196.60gold quality
ganglionic eminenceUBERON:000402395.83gold quality
upper arm skinUBERON:000426395.67gold quality
cortical plateUBERON:000534395.31gold quality
gastrocnemiusUBERON:000138895.27gold quality
stromal cell of endometriumCL:000225595.17gold quality
muscle of legUBERON:000138395.16gold quality
islet of LangerhansUBERON:000000695.03gold quality
calcaneal tendonUBERON:000370195.02gold quality
vermiform appendixUBERON:000115494.99gold quality
cardiac muscle of right atriumUBERON:000337994.95silver quality
sural nerveUBERON:001548894.87gold quality
granulocyteCL:000009494.77gold quality
nasal cavity epitheliumUBERON:000538494.44gold quality
hindlimb stylopod muscleUBERON:000425294.43gold quality
rectumUBERON:000105294.34gold quality
skin of legUBERON:000151194.17gold quality
deltoidUBERON:000147694.14gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047394.01gold quality
left ventricle myocardiumUBERON:000656693.87gold quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099193.67gold quality
colonic epitheliumUBERON:000039793.62gold quality
adrenal glandUBERON:000236993.53gold quality
zone of skinUBERON:000001493.50gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3yes7.33

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

54 targeting EFTUD2, 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-4283100.0066.422097
HSA-MIR-6833-3P100.0070.633197
HSA-MIR-4262100.0073.263931
HSA-MIR-4768-5P100.0069.492861
HSA-MIR-6870-5P99.9968.552115
HSA-MIR-4723-5P99.9768.702034
HSA-MIR-569899.9768.492029
HSA-MIR-7111-5P99.9768.482062
HSA-MIR-129799.9173.413162
HSA-MIR-498-3P99.9171.271114
HSA-MIR-627-3P99.9071.423316
HSA-MIR-26A-5P99.7873.522303
HSA-MIR-26B-5P99.7873.512305
HSA-MIR-430699.7270.503630
HSA-MIR-446599.7172.562096
HSA-MIR-317599.6566.302031
HSA-MIR-3177-5P99.6570.381174
HSA-MIR-432899.5771.064094
HSA-MIR-6716-5P99.5668.621244
HSA-MIR-186-3P99.5166.241685
HSA-MIR-469699.4867.481040
HSA-MIR-127599.4767.902749
HSA-MIR-391599.4568.491905
HSA-MIR-185-5P99.3568.602497
HSA-MIR-464499.3569.122514
HSA-MIR-4685-5P99.2565.991563
HSA-MIR-6837-5P99.2565.471632
HSA-MIR-544B99.1867.411632
HSA-MIR-892C-5P99.1670.562116
HSA-MIR-3127-3P98.9467.341055

Functional genomics

ClinGen dosage: haploinsufficiency 3 (sufficient evidence), triplosensitivity 0 (no evidence). ClinGen Gene Dosage Map DepMap (CRISPR cell-line fitness): dependent in 99.8% of screened cell lines, common-essential.

Literature-anchored findings (GeneRIF, showing 23)

  • Validation studies of eight additional individuals with MFDM demonstrated causative EFTUD2 mutations in all affected individuals tested. (PMID:22305528)
  • EFTUD2 haploinsufficiency leads to syndromic oesophageal atresia. (PMID:23188108)
  • Novel mutations in EFTUD2 were discovered in 3 patients. These mutations expand the clinical features in patients with EFTUD2 mutations and demonstrate an overlap with oculo-auriculo-vertebral spectrum. (PMID:23239648)
  • the phenotype in patients with EFTUD2 mutations is much broader than previously anticipated; in addition to AFD type Guion-Almeida and syndromic esophageal atresia, oto-facial syndrome also belongs to the EFTUD2 mutation spectrum (PMID:23879989)
  • A de nove deletion mutation at 17q21.31, encompassing the EFTUD2 gene, is associated with congenital mandibulofacial dysostosis with microcephaly. (PMID:24266672)
  • Study describes loss-of-function mutations in EFTUD2 gene in patients with different clinical manifestations of Mandibulofacial dysostosis, Guion-Almeida type syndrome. (PMID:24470203)
  • Three different mutations in EFTUD2 gene were found in patients with mandibulofacial dysostosis type Guion-Almeida syndrome (PMID:25387991)
  • Results show that SNW1 directly associates with EFTUD2 and SNRNP200 and that disruption of SNW1 association with these proteins promotes the apoptosis of breast cancer cells. (PMID:25450007)
  • Novel heterozygous mutations in EFTUD2, detected by exome sequencing, in mandibulofacial dysostosis with Microcephaly syndrome. (PMID:25735261)
  • We report a clinical and extensive molecular study, including TCOF1, POLR1D, POLR1C, and EFTUD2 genes, in a series of 146 patients with TCS. (PMID:25790162)
  • These data demonstrate that EFTUD2 restricts Hepatitis C Virus infection mainly through an RIG-I/MDA5-mediated, JAK-STAT-independent pathway, thereby revealing the participation of EFTUD2 as a novel innate immune regulator. (PMID:25878102)
  • An update on mandibulofacial dysostosis with microcephaly and EFTUD2 mutations has been presented. (Review) (PMID:26507355)
  • we report two individuals of Asian ancestry with Mandibulofacial dysostosis type Guion-Almeida (MFDGA), each harboring a novel, pathogenic splice site variant in EFTUD2 (PMID:29381487)
  • report 2 cases of mandibulofacial dysostosis with microcephaly (MFDM) with different and novel de novo mutations in the elongation factor Tu GTP binding domain containing 2 gene (PMID:30343593)
  • EFTUD2 missense variants disrupt protein function and splicing in mandibulofacial dysostosis Guion-Almeida type. (PMID:32333448)
  • Spliceosome protein EFTUD2 is upregulated in the trophoblast of spontaneous miscarriage and hydatidiform mole. (PMID:32447180)
  • A novel EFTUD2 mutation identified an adult male with mandibulofacial dysostosis Guion-Almeida type. (PMID:32541334)
  • EFTUD2 maintains the survival of tumor cells and promotes hepatocellular carcinoma progression via the activation of STAT3. (PMID:33024090)
  • Mandibulofacial dysostosis with microcephaly: An expansion of the phenotype via parental survey. (PMID:33247512)
  • Association of Elongation Factor Tu GTP-binding Domain-containing 2 Gene (EFTUD2) Polymorphism with the Risk of Hepatitis B Virus Infection. (PMID:34436958)
  • The Pregnancy Zone Protein (PZP) is significantly downregulated in the placenta of preeclampsia and HELLP syndrome patients. (PMID:35843132)
  • The Spliceosome Factor EFTUD2 Promotes IFN Anti-HBV Effect through mRNA Splicing. (PMID:37396299)
  • Identification of novel mutations in EYA3 and EFTUD2 in a family with craniofacial microsomia: evidence of digenic inheritance. (PMID:37507637)

Cross-species orthologs

5 orthologs

OrganismSymbolGene ID
danio_rerioeftud2ENSDARG00000012261
mus_musculusEftud2ENSMUSG00000020929
rattus_norvegicusEftud2ENSRNOG00000002818
drosophila_melanogasterCG4849FBGN0039566
caenorhabditis_elegansWBGENE00001166

Paralogs (18): MTIF2 (ENSG00000085760), GTPBP1 (ENSG00000100226), EEF1A2 (ENSG00000101210), GSPT1 (ENSG00000103342), HBS1L (ENSG00000112339), EIF2S3 (ENSG00000130741), EEFSEC (ENSG00000132394), EFL1 (ENSG00000140598), GUF1 (ENSG00000151806), EEF1A1 (ENSG00000156508), EIF5B (ENSG00000158417), GFM2 (ENSG00000164347), EEF2 (ENSG00000167658), GFM1 (ENSG00000168827), GTPBP2 (ENSG00000172432), TUFM (ENSG00000178952), EIF2S3B (ENSG00000180574), GSPT2 (ENSG00000189369)

Protein

Protein identifiers

116 kDa U5 small nuclear ribonucleoprotein componentQ15029 (reviewed: Q15029)

Alternative names: Elongation factor Tu GTP-binding domain-containing protein 2, SNU114 homolog, U5 snRNP-specific protein, 116 kDa

All UniProt accessions (7): Q15029, K7EIT3, K7EIV5, K7EJ74, K7EP67, K7EQ26, K7ERJ5

UniProt curated annotations — full annotation on UniProt →

Function. Required for pre-mRNA splicing as component of the spliceosome, including pre-catalytic, catalytic and post-catalytic spliceosomal complexes. Component of the U5 snRNP and the U4/U6-U5 tri-snRNP complex, a building block of the spliceosome. As a component of the minor spliceosome, involved in the splicing of U12-type introns in pre-mRNAs.

Subunit / interactions. Component of the U5 snRNP and the U4/U6-U5 tri-snRNP complex, a building block of the spliceosome. The U4/U6-U5 tri-snRNP complex is composed of the U4, U6 and U5 snRNAs and at least PRPF3, PRPF4, PRPF6, PRPF8, PRPF31, SNRNP200, TXNL4A, SNRNP40, DDX23, CD2BP2, PPIH, SNU13, EFTUD2, SART1 and USP39. Component of the pre-catalytic, catalytic and post-catalytic spliceosome complexes. Component of the minor spliceosome, which splices U12-type introns. Within this complex, interacts with CRIPT. Interacts with ERBB4 and PRPF8. Interacts with PIH1D1. Interacts with RPAP3 and URI1 in a ZNHIT2-dependent manner. Interacts with NRDE2. Interacts with FAM50A. Interacts with UBL5.

Subcellular location. Nucleus.

Disease relevance. Mandibulofacial dysostosis with microcephaly (MFDM) [MIM:610536] A rare syndrome characterized by progressive microcephaly, midface and malar hypoplasia, micrognathia, microtia, dysplastic ears, preauricular skin tags, significant developmental delay, and speech delay. Many patients have major sequelae, including choanal atresia that results in respiratory difficulties, conductive hearing loss, and cleft palate. The disease is caused by variants affecting the gene represented in this entry.

Similarity. Belongs to the TRAFAC class translation factor GTPase superfamily. Classic translation factor GTPase family. EF-G/EF-2 subfamily.

Isoforms (3)

UniProt IDNamesCanonical?
Q15029-11yes
Q15029-22
Q15029-33

RefSeq proteins (4): NP_001136077, NP_001245282, NP_001245283, NP_004238* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR000640EFG_V-likeDomain
IPR000795T_Tr_GTP-bd_domDomain
IPR004161EFTu-like_2Domain
IPR005225Small_GTP-bdDomain
IPR005517Transl_elong_EFG/EF2_IVDomain
IPR009000Transl_B-barrel_sfHomologous_superfamily
IPR014721Ribsml_uS5_D2-typ_fold_subgrHomologous_superfamily
IPR020568Ribosomal_Su5_D2-typ_SFHomologous_superfamily
IPR027417P-loop_NTPaseHomologous_superfamily
IPR031950EFTUD2_NDomain
IPR035647EFG_III/VHomologous_superfamily
IPR035655U5-116kDa_CDomain
IPR041095EFG_IIDomain
IPR044121Snu114_GTP-bdDomain

Pfam: PF00009, PF00679, PF03144, PF03764, PF14492, PF16004

UniProt features (125 total): strand 54, helix 32, turn 17, sequence variant 4, modified residue 3, sequence conflict 3, binding site 3, cross-link 2, splice variant 2, compositionally biased region 2, chain 1, domain 1, region of interest 1

Structure

Experimental structures (PDB)

68 structures, top 30 by resolution.

PDBMethodResolution (Å)
8H6LELECTRON MICROSCOPY2.6
8H6KELECTRON MICROSCOPY2.7
8C6JELECTRON MICROSCOPY2.8
6ID1ELECTRON MICROSCOPY2.86
7DVQELECTRON MICROSCOPY2.89
6ID0ELECTRON MICROSCOPY2.9
6QW6ELECTRON MICROSCOPY2.92
6ICZELECTRON MICROSCOPY3
8I0RELECTRON MICROSCOPY3
8I0TELECTRON MICROSCOPY3
8I0VELECTRON MICROSCOPY3
7QTTELECTRON MICROSCOPY3.1
8Q7NELECTRON MICROSCOPY3.1
8Q91ELECTRON MICROSCOPY3.1
8QOZELECTRON MICROSCOPY3.1
8QPEELECTRON MICROSCOPY3.1
9R3DELECTRON MICROSCOPY3.12
8H6EELECTRON MICROSCOPY3.2
8Q7QELECTRON MICROSCOPY3.2
8RC0ELECTRON MICROSCOPY3.2
8H6JELECTRON MICROSCOPY3.25
6QX9ELECTRON MICROSCOPY3.28
6QDVELECTRON MICROSCOPY3.3
8I0UELECTRON MICROSCOPY3.3
9FMDELECTRON MICROSCOPY3.3
8Y6OELECTRON MICROSCOPY3.38
6FF4ELECTRON MICROSCOPY3.4
6ZYMELECTRON MICROSCOPY3.4
8I0PELECTRON MICROSCOPY3.4
8I0WELECTRON MICROSCOPY3.4

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q15029-F189.940.76

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 (3): 136–143; 204–208; 258–261

Post-translational modifications (5): 86, 64, 64, 1, 19

Function

Pathways and Gene Ontology

Reactome pathways

3 pathways

IDPathway
R-HSA-72163mRNA Splicing - Major Pathway
R-HSA-72165mRNA Splicing - Minor Pathway
R-HSA-9918481Dengue Virus-Host Interactions

MSigDB gene sets: 293 (showing top): GOBP_RESPONSE_TO_NITROGEN_COMPOUND, GOBP_RESPONSE_TO_COCAINE, GOBP_NEGATIVE_REGULATION_OF_RNA_SPLICING, MODULE_150, USF_C, MODULE_388, GOBP_RESPONSE_TO_ALKALOID, GOBP_SPLICEOSOMAL_TRI_SNRNP_COMPLEX_ASSEMBLY, MODULE_195, MARTINEZ_RB1_TARGETS_DN, REACTOME_PROCESSING_OF_CAPPED_INTRON_CONTAINING_PRE_MRNA, GOBP_PROTEIN_RNA_COMPLEX_ORGANIZATION, GOBP_RESPONSE_TO_OXYGEN_CONTAINING_COMPOUND, GOBP_RNA_SPLICING, REACTOME_MRNA_SPLICING

GO Biological Process (5): mRNA splicing, via spliceosome (GO:0000398), response to cocaine (GO:0042220), cellular response to xenobiotic stimulus (GO:0071466), mRNA processing (GO:0006397), RNA splicing (GO:0008380)

GO Molecular Function (6): RNA binding (GO:0003723), GTPase activity (GO:0003924), GTP binding (GO:0005525), U5 snRNA binding (GO:0030623), nucleotide binding (GO:0000166), protein binding (GO:0005515)

GO Cellular Component (11): nucleus (GO:0005634), nucleoplasm (GO:0005654), spliceosomal complex (GO:0005681), cytosol (GO:0005829), Cajal body (GO:0015030), membrane (GO:0016020), nuclear speck (GO:0016607), U4/U6 x U5 tri-snRNP complex (GO:0046540), U2-type precatalytic spliceosome (GO:0071005), U2-type catalytic step 2 spliceosome (GO:0071007), catalytic step 2 spliceosome (GO:0071013)

Reactome top-level categories

Rollup of top-2 pathways:

CategoryPathways
mRNA Splicing2
Dengue Virus Infection1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cellular anatomical structure3
RNA processing2
nuclear ribonucleoprotein granule2
U5 snRNP2
U2-type spliceosomal complex2
U2 snRNP2
RNA splicing, via transesterification reactions with bulged adenosine as nucleophile1
mRNA processing1
response to alkaloid1
response to oxygen-containing compound1
response to xenobiotic stimulus1
cellular response to chemical stimulus1
mRNA metabolic process1
nucleic acid binding1
ribonucleoside triphosphate phosphatase activity1
guanyl ribonucleotide binding1
purine ribonucleoside triphosphate binding1
snRNA binding1
nucleoside phosphate binding1
heterocyclic compound binding1
binding1
intracellular membrane-bounded organelle1
nuclear lumen1
nuclear protein-containing complex1
ribonucleoprotein complex1
cytoplasm1
U4/U6 snRNP1
spliceosomal tri-snRNP complex1
U1 snRNP1
U4/U6 x U5 tri-snRNP complex1
precatalytic spliceosome1
U6 snRNP1
catalytic step 2 spliceosome1
Prp19 complex1
spliceosomal complex1
catalytic complex1

Protein interactions and networks

STRING

6375 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
EFTUD2SNRNP200O75643982
EFTUD2PRPF8Q6P2Q9970
EFTUD2SRRM2Q9UQ35916
EFTUD2AAR2Q9Y312916
EFTUD2PRPF6O94906847
EFTUD2SF3B3Q15393844
EFTUD2PRPF31Q8WWY3844
EFTUD2SNRNP40Q96DI7834
EFTUD2PRPF3O43395822
EFTUD2SF3B1O75533821
EFTUD2SF3A3Q12874810
EFTUD2SF3B4Q15427803
EFTUD2CDC5LQ99459783
EFTUD2TXNL4AP83876782
EFTUD2SF3B2Q13435778
EFTUD2SNU13P55769778

IntAct

251 interactions, top by confidence:

ABTypeScore
EFTUD2PRPF8psi-mi:“MI:0915”(physical association)0.900
PRPF8EFTUD2psi-mi:“MI:0915”(physical association)0.900
EFTUD2PRPF6psi-mi:“MI:0915”(physical association)0.880
EFTUD2SNRNP40psi-mi:“MI:0915”(physical association)0.810
EFTUD2SNRNP200psi-mi:“MI:0915”(physical association)0.790
SNRNP200EFTUD2psi-mi:“MI:0915”(physical association)0.790
PRPF6SNRNP200psi-mi:“MI:0914”(association)0.770
SNRPEGEMIN2psi-mi:“MI:0914”(association)0.770
PRPF8SNRNP200psi-mi:“MI:0915”(physical association)0.740
PRPF3PRPF4psi-mi:“MI:0914”(association)0.730
CFTRESYT2psi-mi:“MI:2364”(proximity)0.710
SNRPD2GEMIN2psi-mi:“MI:0914”(association)0.710
SNRPGGEMIN2psi-mi:“MI:0914”(association)0.710
MYCEFTUD2psi-mi:“MI:0915”(physical association)0.680
EFTUD2MYCpsi-mi:“MI:0915”(physical association)0.680
UBL5SART1psi-mi:“MI:0914”(association)0.670
HSP90AA1CHUKpsi-mi:“MI:0914”(association)0.670
SNRPBPRMT5psi-mi:“MI:0914”(association)0.670
HSF1KPNA3psi-mi:“MI:0914”(association)0.640
NCBP2KPNA3psi-mi:“MI:0914”(association)0.640
NCBP1KPNA3psi-mi:“MI:0914”(association)0.640
PRPF8PRPF4psi-mi:“MI:0914”(association)0.640
SF3B1SAP18psi-mi:“MI:0914”(association)0.640

BioGRID (1845): EFTUD2 (Affinity Capture-MS), PRPF8 (Two-hybrid), EFTUD2 (Affinity Capture-RNA), EFTUD2 (Affinity Capture-MS), EFTUD2 (Affinity Capture-MS), EFTUD2 (Affinity Capture-MS), EFTUD2 (Affinity Capture-MS), EFTUD2 (Affinity Capture-MS), EFTUD2 (Affinity Capture-MS), EFTUD2 (Affinity Capture-MS), EFTUD2 (Affinity Capture-MS), EFTUD2 (Affinity Capture-MS), EFTUD2 (Affinity Capture-MS), EFTUD2 (Affinity Capture-MS), EFTUD2 (Affinity Capture-MS)

ESM2 similar proteins: A1JJ92, A1RH82, A3MYA2, A3QGT8, A4FUD3, A4TQJ9, A4W691, A5F904, A6QLJ3, A7FMI1, A7MUW8, A8FYR3, A8H733, A9R055, B0BRI9, B0TQ95, B0USE8, B1JL43, B1KRQ3, B2K3I2, B3GZM0, B4EWB0, B4RU35, B6ENF7, C3LSR4, C5BHI4, C6DJU6, F4JWP9, O08810, P43928, Q0I2G9, Q12QG7, Q15029, Q1C156, Q1CMZ7, Q2S9X0, Q3IHI5, Q487B0, Q5F3X4, Q5QXU1

Diamond homologs: A0B7D5, A0RW30, A0SXL6, A1RVX2, A3CXM8, A3DMV6, A3MSN3, A4FUD3, A4WMR8, A4YCV9, A5DI11, A5ULM6, A7I4X4, A8ACA7, B0R8C8, B1L7Q0, B1YE08, B6YVG5, B8D6B2, B8GJK8, C3MQ53, C3MVH1, C3N5S0, C3NED6, C3NHB6, C4KHE9, C4YJQ8, C5A6N7, C6A4M0, C7NYH7, D3E3N9, F4JWP9, O08810, O14460, O23755, O27131, O28385, O59521, O74945, O93632

SIGNOR signaling

1 interactions.

AEffectBMechanism
EFTUD2“form complex”“U4/U6.U5 snRNP complex”binding

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 208 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 RNA833.4×3e-09
mRNA Splicing - Minor Pathway1522.1×8e-15
mRNA Splicing2820.2×7e-27
mRNA Splicing - Major Pathway4917.6×7e-46
Abortive elongation of HIV-1 transcript in the absence of Tat516.3×3e-04
Processing of Capped Intron-Containing Pre-mRNA3016.2×5e-26
RNA Polymerase II Transcription Termination1014.4×9e-08
mRNA Polyadenylation2313.3×1e-17

GO biological processes:

GO termPartnersFoldFDR
spliceosomal tri-snRNP complex assembly742.3×2e-08
RNA splicing, via transesterification reactions1136.9×1e-12
spliceosomal snRNP assembly1134.4×2e-12
U2-type prespliceosome assembly1033.6×4e-11
spliceosomal complex assembly1032.4×5e-11
mRNA cis splicing, via spliceosome526.6×1e-04
regulation of mRNA splicing, via spliceosome523.8×2e-04
mRNA splicing, via spliceosome4522.2×2e-45

Disease & clinical

Cancer significance

From intOGen — cancer-driver classification: activating (oncogene-like) across 1 cancer types — PCM.

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic99
Likely pathogenic70
Uncertain significance294
Likely benign281
Benign98

Top pathogenic / likely-pathogenic (30)

Variant IDHGVSClassification
1029804NM_004247.4(EFTUD2):c.1331del (p.Gly444fs)Pathogenic
1029805NM_004247.4(EFTUD2):c.378del (p.Glu127fs)Pathogenic
1175913NM_004247.4(EFTUD2):c.1150-1G>TPathogenic
1364366NM_004247.4(EFTUD2):c.702+1delPathogenic
1409617NM_004247.4(EFTUD2):c.1920_1923dup (p.His642fs)Pathogenic
1431432NM_004247.4(EFTUD2):c.158del (p.Pro53fs)Pathogenic
1433437NM_004247.4(EFTUD2):c.1402dup (p.Cys468fs)Pathogenic
1454611NM_004247.4(EFTUD2):c.2562-2delPathogenic
1526579GRCh37/hg19 17q21.31(chr17:42953220-42972444)Pathogenic
1679931NM_004247.4(EFTUD2):c.3G>T (p.Met1Ile)Pathogenic
1693035NM_004247.4(EFTUD2):c.1127C>G (p.Pro376Arg)Pathogenic
1698725NM_004247.4(EFTUD2):c.1719+1G>APathogenic
1702966NM_004247.4(EFTUD2):c.2199G>A (p.Trp733Ter)Pathogenic
1703337NM_004247.4(EFTUD2):c.1705C>T (p.Arg569Ter)Pathogenic
1706532NM_004247.4(EFTUD2):c.423del (p.Lys142fs)Pathogenic
1804926NM_004247.4(EFTUD2):c.509_519del (p.Ile170fs)Pathogenic
2002395NM_004247.4(EFTUD2):c.1888del (p.Leu630fs)Pathogenic
203386NM_004247.4(EFTUD2):c.764dup (p.Cys256fs)Pathogenic
2100276NM_004247.4(EFTUD2):c.1513C>T (p.Gln505Ter)Pathogenic
210914NM_004247.4(EFTUD2):c.1149+1G>CPathogenic
210915NM_004247.4(EFTUD2):c.1297_1298del (p.Met433fs)Pathogenic
2446031NM_004247.4(EFTUD2):c.1012G>T (p.Glu338Ter)Pathogenic
2498220NM_004247.4(EFTUD2):c.593dup (p.Tyr198Ter)Pathogenic
2506543GRCh37/hg19 17q21.31(chr17:42929777-42937911)Pathogenic
2581074NM_004247.4(EFTUD2):c.2643_2649del (p.Phe881fs)Pathogenic
265116NM_004247.4(EFTUD2):c.2698_2701del (p.Val900fs)Pathogenic
265311NM_004247.4(EFTUD2):c.1860+2delPathogenic
2662935NM_004247.4(EFTUD2):c.2330G>T (p.Gly777Val)Pathogenic
2687899NM_004247.4(EFTUD2):c.1421del (p.Leu474fs)Pathogenic
2710262NM_004247.4(EFTUD2):c.671G>T (p.Gly224Val)Pathogenic

SpliceAI

3677 predictions. Top by Δscore:

VariantEffectΔscore
17:44851366:GGCC:Gacceptor_gain1.0000
17:44851368:CC:Cacceptor_gain1.0000
17:44851369:CC:Cacceptor_gain1.0000
17:44851370:C:CCacceptor_gain1.0000
17:44851370:CTG:Cacceptor_loss1.0000
17:44851371:T:Aacceptor_loss1.0000
17:44851705:CATA:Cdonor_loss1.0000
17:44851706:ATACC:Adonor_loss1.0000
17:44851707:TAC:Tdonor_loss1.0000
17:44851708:ACCTT:Adonor_gain1.0000
17:44851709:C:Gdonor_loss1.0000
17:44851709:CCTTC:Cdonor_gain1.0000
17:44851712:T:Adonor_gain1.0000
17:44851813:ACAAT:Aacceptor_gain1.0000
17:44851814:CAAT:Cacceptor_gain1.0000
17:44851814:CAATC:Cacceptor_gain1.0000
17:44851815:AAT:Aacceptor_gain1.0000
17:44851816:AT:Aacceptor_gain1.0000
17:44851817:TCTAA:Tacceptor_loss1.0000
17:44851818:C:CCacceptor_gain1.0000
17:44851818:CTAAA:Cacceptor_loss1.0000
17:44852403:TCTCA:Tdonor_loss1.0000
17:44852404:CTCA:Cdonor_loss1.0000
17:44852405:TCA:Tdonor_loss1.0000
17:44852406:CA:Cdonor_loss1.0000
17:44852408:C:CTdonor_loss1.0000
17:44852558:GCCCC:Gacceptor_gain1.0000
17:44852559:CCCC:Cacceptor_gain1.0000
17:44852559:CCCCC:Cacceptor_gain1.0000
17:44852560:CCC:Cacceptor_gain1.0000

AlphaMissense

6450 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
17:44851365:A:GL943P1.000
17:44851369:C:GG942R1.000
17:44851713:C:AR940S1.000
17:44851713:C:GR940S1.000
17:44851714:C:AR940M1.000
17:44851714:C:GR940T1.000
17:44851717:C:GR939P1.000
17:44851720:C:GR938P1.000
17:44851721:G:TR938S1.000
17:44851744:G:TA930D1.000
17:44852461:C:GR888P1.000
17:44852464:A:GL887P1.000
17:44852530:C:TG865D1.000
17:44852560:C:TG855E1.000
17:44852561:C:AG855W1.000
17:44852561:C:GG855R1.000
17:44852561:C:TG855R1.000
17:44853296:C:AR854M1.000
17:44853296:C:GR854T1.000
17:44853389:G:TA823D1.000
17:44853390:C:GA823P1.000
17:44853521:A:GL821P1.000
17:44853545:C:AR813M1.000
17:44853545:C:GR813T1.000
17:44854280:A:GL779P1.000
17:44854286:C:TG777D1.000
17:44854287:C:GG777R1.000
17:44854310:C:TG769D1.000
17:44854311:C:GG769R1.000
17:44854566:A:TL750Q1.000

dbSNP variants (sampled 300 via entrez): RS1000027322 (17:44882631 T>C), RS1000188945 (17:44888803 T>A,C), RS1000256102 (17:44877642 C>T), RS1000281618 (17:44871261 G>A), RS1000337987 (17:44854414 G>A), RS1000348735 (17:44894307 T>C,G), RS1000382466 (17:44890162 C>G), RS1000398052 (17:44871498 C>A,G), RS1000423862 (17:44894697 A>T), RS1000495182 (17:44865243 C>T), RS1000545149 (17:44859653 A>ACG), RS1000594635 (17:44858830 C>T), RS1000627959 (17:44877391 G>A), RS1000806640 (17:44894317 C>G), RS1000829265 (17:44852618 A>C)

Disease associations

OMIM: gene MIM:603892 | disease phenotypes: MIM:610536, MIM:610805, MIM:189960

GenCC curated gene-disease

DiseaseClassificationInheritance
mandibulofacial dysostosis-microcephaly syndromeDefinitiveAutosomal dominant

ClinGen Gene-Disease Validity (1)

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

DiseaseClassificationInheritance
mandibulofacial dysostosis-microcephaly syndromeDefinitiveAD

Mondo (7): mandibulofacial dysostosis-microcephaly syndrome (MONDO:0012516), mandibulofacial dysostosis (MONDO:0015483), cleft lip/palate (MONDO:0016044), congenital anomaly of kidney and urinary tract (MONDO:0019719), esophageal atresia (MONDO:0001044), neurodevelopmental disorder (MONDO:0700092), esophageal atresia/tracheoesophageal fistula (MONDO:0008586)

Orphanet (6): Mandibulofacial dysostosis-microcephaly syndrome (Orphanet:79113), Genetic syndromic Pierre Robin syndrome (Orphanet:363294), Mandibulofacial dysostosis (Orphanet:155899), Cleft lip/palate (Orphanet:199306), Renal or urinary tract malformation (Orphanet:93545), Esophageal atresia (Orphanet:1199)

HPO phenotypes

46 total (30 of 46 shown, HPO-id order):

HPOTerm
HP:0000006Autosomal dominant inheritance
HP:0000175Cleft palate
HP:0000191Accessory oral frenulum
HP:0000243Trigonocephaly
HP:0000252Microcephaly
HP:0000253Progressive microcephaly
HP:0000272Malar flattening
HP:0000286Epicanthus
HP:0000327Hypoplasia of the maxilla
HP:0000347Micrognathia
HP:0000356Abnormality of the outer ear
HP:0000369Low-set ears
HP:0000384Preauricular skin tag
HP:0000396Overfolded helix
HP:0000405Conductive hearing impairment
HP:0000413Atresia of the external auditory canal
HP:0000453Choanal atresia
HP:0000463Anteverted nares
HP:0000494Downslanted palpebral fissures
HP:0000506Telecanthus
HP:0000582Upslanted palpebral fissure
HP:0000750Delayed speech and language development
HP:0001177Preaxial hand polydactyly
HP:0001238Slender finger
HP:0001249Intellectual disability
HP:0001250Seizure
HP:0001263Global developmental delay
HP:0001629Ventricular septal defect
HP:0001631Atrial septal defect
HP:0002002Deep philtrum

GWAS associations

2 associations (top):

StudyTraitp-value
GCST004412_12Craniofacial microsomia9.000000e-06
GCST008916_39Asthma8.000000e-12

MeSH disease descriptors (6)

DescriptorNameTree numbers
D004933Esophageal AtresiaC06.198.330; C06.405.117.260; C16.131.314.330
D008342Mandibulofacial DysostosisC05.116.099.370.231.576; C05.660.207.231.576; C11.270.147.750; C16.131.621.207.231.576
D065886Neurodevelopmental DisordersF03.625
C566906Cakut (supp.)
C531835Esophageal atresia with or without tracheoesophageal fistula (supp.)
C537405Growth and mental retardation, mandibulofacial dysostosis, microcephaly, and cleft palate (supp.)

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL5725038 (SINGLE PROTEIN)

Molecules with ChEMBL bioactivity

1 molecules (phase ≥1), by development phase (incl. off-target/promiscuous compounds). Patent mentions across the top 20 by phase: 1,538 (via chembl_molecule»patent_compound — counts attach to the compound, not the gene–compound relationship, so off-target/promiscuous molecules can dominate).

MoleculeNamePhasePatents
CHEMBL1232461MOLIBRESIB21,538

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

ChEMBL bioactivities

5 potent at pChembl≥5 of 5 total, top 5 by pChembl (potency: 10 = 0.1 nM, 6 = 1 µM).

pChemblTypeValueUnitMolecule
7.23Kd59.32nMCHEMBL5653589
7.23ED5059.32nMCHEMBL5653589
7.07Kd85nMMOLIBRESIB
6.97Kd108.2nMCHEMBL3752910
6.97ED50108.2nMCHEMBL3752910

PubChem BioAssay actives

3 with measured affinity, of 11 total; 3 most potent distinct compounds. Largely complementary to BindingDB; screening values are coarse (µM, 4 dp), so sub-nM hits tie at the floor.

CompoundAssayTypeValueUnit
4-methyl-3-[(2-methyl-6-pyridin-3-ylpyrazolo[3,4-d]pyrimidin-4-yl)amino]-N-[3-(trifluoromethyl)phenyl]benzamide2148291: Binding affinity to human EFTUD2 incubated for 45 mins by Kinobead based pull down assaykd0.0593uM
2-[(4S)-6-(4-chlorophenyl)-8-methoxy-1-methyl-4H-[1,2,4]triazolo[4,3-a][1,4]benzodiazepin-4-yl]-N-ethylacetamide2179080: Binding affinity against EFTUD2 (unknown origin) assessed as apparent dissociation constant incubated for 1 hr by colloidal coomassie staining based LC-MS/MS analysiskd0.0850uM
4-methyl-3-[(1-methyl-6-pyridin-3-ylpyrazolo[3,4-d]pyrimidin-4-yl)amino]-N-[3-(trifluoromethyl)phenyl]benzamide2148291: Binding affinity to human EFTUD2 incubated for 45 mins by Kinobead based pull down assaykd0.1082uM

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
bisphenol Aincreases expression, affects cotreatment, decreases expression2
sodium arsenitedecreases expression, increases expression2
Particulate Matterincreases expression2
FR900359increases phosphorylation1
TAK-243decreases sumoylation1
alpha-pineneincreases abundance, affects cotreatment, increases oxidation1
beta-lapachonedecreases expression1
tetrabromobisphenol Adecreases expression1
methacrylaldehydeincreases abundance, affects cotreatment, increases oxidation1
yessotoxindecreases expression1
4-phenylbutyric aciddecreases expression1
2,3,5-(triglutathion-S-yl)hydroquinoneincreases ADP-ribosylation1
CGP 52608affects binding, increases reaction1
AM 251decreases expression1
nutlin 3affects cotreatment, increases secretion1
ICG 001decreases expression1
bisphenol Bincreases expression1
bisphenol Sincreases expression1
PP242decreases expression1
bisphenol AFincreases expression1
4-(4-((5-(4,5-dimethyl-2-nitrophenyl)-2-furanyl)methylene)-4,5-dihydro-3-methyl-5-oxo-1H-pyrazol-1-yl)benzoic aciddecreases expression1
Resveratrolincreases phosphorylation1
Acetaminophenaffects response to substance1
Acroleinaffects cotreatment, increases oxidation, increases abundance1
Air Pollutantsincreases abundance, increases oxidation, affects cotreatment1
Vehicle Emissionsincreases expression1
Benzo(a)pyreneincreases expression1
Caffeinedecreases phosphorylation1
Coumestrolincreases expression1
Dactinomycinaffects cotreatment, increases secretion1

ChEMBL screening assays

8 unique, capped per target: 8 binding

Representative assays (with source publication via chembl_document):

Assay IDTypeDescriptionSource paper
CHEMBL5651333BindingBinding affinity to human EFTUD2 incubated for 45 mins by Kinobead based pull down assayNVP-BHG712: Effects of Regioisomers on the Affinity and Selectivity toward the EPHrin Family. — ChemMedChem

Clinical trials (associated diseases)

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

TrialPhaseStatusTitle
NCT04234971PHASE4RECRUITINGCost Effectiveness in Alveolar Bone Grafting in Patients With Cleft Lip and Palate
NCT04771156PHASE4RECRUITINGKetorolac in Palatoplasty
NCT04586348PHASE4UNKNOWNPrenatal Iodine Supplementation and Early Childhood Neurodevelopment
NCT04873115PHASE4UNKNOWNDouble-blind, Placebo-controlled, Randomized Clinical Trial Comparing the Efficacy and Safety of Sialanar Plus orAl rehabiLitation Against Placebo Plus Oral Rehabilitation for chIldren and Adolescents With seVere Sialorrhoea and Neurodisabilties,
NCT03766217PHASE3COMPLETEDBone Tissue Engineering With Dental Pulp Stem Cells for Alveolar Cleft Repair
NCT06284434PHASE3RECRUITINGLiposomal Bupivacaine Use in Alveolar Bone Graft Patients
NCT00226044PHASE3COMPLETEDRectal and Oral Omeprazole Treatment of Reflux Disease in Infants.
NCT02559102PHASE3COMPLETEDDexmedetomidine Sedation Versus General Anaesthesia for Inguinal Hernia Surgery in Infants
NCT02757079PHASE3COMPLETEDStudy of the Efficacy and Safety of NPC-15 for Sleep Disorders of Children With Neurodevelopmental Disorders
NCT06915480PHASE3RECRUITINGReducing Missed Appointments
NCT07377032PHASE3RECRUITINGTAP-GRIN: Interventional Study on Patients With GRIN-related Neurodevelopmental Disorders
NCT00930124PHASE2COMPLETEDCleft Orthognathic Surgery Versus Distraction Osteogenesis - Which is Better?
NCT03127345PHASE2WITHDRAWNOmega 3 Fatty Acid Treatment for Pediatric Musculoskeletal Health
NCT02909959PHASE2COMPLETEDSulforaphane for the Treatment of Young Men With Autism Spectrum Disorder
NCT06081348PHASE2RECRUITINGSertraline vs. Placebo in the Treatment of Anxiety in Children and AdoLescents With NeurodevelopMental Disorders
NCT06352372PHASE2COMPLETEDSafety and Efficacy of tPBM for Epileptiform Activity in Autism
NCT04115345PHASE1COMPLETEDA Study of a Renal Autologous Cell Therapy (REACT) in Patients With Chronic Kidney Disease (CKD) From Congenital Anomalies of the Kidney and Urinary Tract (CAKUT).
NCT05694169PHASE1TERMINATEDA Study of Participants With Chronic Kidney Disease Previously Treated With REACT
NCT00503191PHASE1COMPLETEDNeuroModulation Technique Treatment of Autism
NCT04475848PHASE1COMPLETEDA Study to Investigate the Safety, Tolerability, Pharmacokinetics, Pharmacodynamics and Food Effect of RO6953958 in Healthy Participants
NCT06300398PHASE1COMPLETEDIAMA-6 Oral Dose Study in Healthy Adults
NCT06408337PHASE1/PHASE2RECRUITINGPhase I-IIa, to Evaluate the Safety, Feasibility, and Efficacy of the Use of BIOCLEFT in the Treatment of Cleft Palate.
NCT00070811Not specifiedCOMPLETEDAssessing the Results of Lip Surgery in Patients With Cleft Lip and Palate
NCT00156442Not specifiedCOMPLETEDA Study to Examine the Relationship Between Sleep Apnea and Cleft Lip/Palate
NCT01601171Not specifiedRECRUITINGGenetics of Reproductive Disorders (Including Kallmann Syndrome) and Cleft Lip and/or Palate
NCT01871623Not specifiedUNKNOWNOne-Piece Le Fort I Osteotomy Versus Segmental Le Fort I Osteotomy
NCT01932164Not specifiedCOMPLETEDUse of Mesenchymal Stem Cells for Alveolar Bone Tissue Engineering for Cleft Lip and Palate Patients
NCT02702869Not specifiedENROLLING_BY_INVITATIONAllied Cleft & Craniofacial Quality-Improvement and Research Network (ACCQUIREnet)
NCT02789787Not specifiedCOMPLETEDClinical Effectiveness of Late Maxillary Protraction for Cleft Lip and Palate
NCT02845193Not specifiedCOMPLETEDEffect of Novel Nasoalveolar Molding Techniques on Parents’ Satisfaction and Short Term Treatment Outcomes in Unilateral Cleft Lip and Palate Infants: A Randomized Controlled Trial
NCT02881606Not specifiedCOMPLETEDEvaluation of the Clinical Effectiveness of Naso-alveolar Molding (NAM) Versus Computer Aided Design NAM (CAD/NAM) in Infants With Bilateral Cleft Lip and Palate: A Randomized Clinical Trial
NCT03011489Not specifiedUNKNOWNParent’s Satisfaction and Evaluation of Postsurgical Outcomes in Unilateral Cleft Lip / Palate Newly Born Infants With / Without Vacuum Formed Nasoalveolar Molding Aligners : A Controlled Clinical Trial
NCT03065686Not specifiedRECRUITINGIdentification of Genetic Factors Implicated in Orofacial Cleft Using Whole Exome Sequencing
NCT03165331Not specifiedUNKNOWNOnline Psychosocial Support for Young People With a Visible Difference: A Randomised Control Study
NCT03217890Not specifiedUNKNOWNthe Relationship Between Cleft Lip and / or Palate (Different Types) and ABO Blood Groups.
NCT03308266Not specifiedCOMPLETEDElectromyographic Analysis of the Masticatory Muscles in Cleft Lip and Palate Children With Temporomandibular Disorders
NCT03395015Not specifiedCOMPLETEDEfficacy of Maxillo-facial Treatment on Cleft Lip and Palate Patients Faces: Aesthetic Considerations
NCT03514563Not specifiedTERMINATEDThree Dimensional Facial Growth Analysis
NCT03563495Not specifiedCOMPLETEDTissue Engineered Constructs for Alveolar Cleft Repair
NCT03582111Not specifiedCOMPLETEDUltrasound Diagnosis of Cleft Lip and Palate