LAGE3 (L antigen family member 3)

Gene

• Entrez ID: 8270
• Gene name: L antigen family member 3
• Gene symbol: LAGE3
• Synonyms (NCBI Gene): CVG5, DXS9879E, DXS9951E, ESO3, GAMOS2, ITBA2, Pcc1
• Chromosome: X
• Chromosome location: Xq28
• Summary: This gene belongs to the ESO/LAGE gene family, members of which are clustered together on chromosome Xq28, and have similar exon-intron structures. Unlike the other family members which are normally expressed only in testis and activated in a wide range o

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs1557211306	C>A	Pathogenic	Missense variant, coding sequence variant
rs1557211410	C>T	Pathogenic	Splice donor variant

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT1103148	hsa-miR-1915	CLIP-seq
MIRT1103149	hsa-miR-2392	CLIP-seq
MIRT1103150	hsa-miR-3074-5p	CLIP-seq
MIRT1103151	hsa-miR-3157-3p	CLIP-seq
MIRT1103152	hsa-miR-3673	CLIP-seq
MIRT1103153	hsa-miR-4286	CLIP-seq
MIRT1103154	hsa-miR-4318	CLIP-seq
MIRT1103155	hsa-miR-4494	CLIP-seq
MIRT1103156	hsa-miR-4533	CLIP-seq
MIRT1103157	hsa-miR-4648	CLIP-seq
MIRT1103158	hsa-miR-4654	CLIP-seq
MIRT1103159	hsa-miR-4722-3p	CLIP-seq
MIRT1103160	hsa-miR-4726-3p	CLIP-seq
MIRT1103161	hsa-miR-4733-3p	CLIP-seq
MIRT1103162	hsa-miR-4747-5p	CLIP-seq
MIRT1103163	hsa-miR-4769-5p	CLIP-seq
MIRT1103164	hsa-miR-499a-5p	CLIP-seq
MIRT1103165	hsa-miR-521	CLIP-seq
MIRT1103166	hsa-miR-562	CLIP-seq
MIRT1103167	hsa-miR-646	CLIP-seq
MIRT1103168	hsa-miR-890	CLIP-seq
MIRT1103149	hsa-miR-2392	CLIP-seq
MIRT2028205	hsa-miR-3200-5p	CLIP-seq
MIRT2028206	hsa-miR-4251	CLIP-seq
MIRT2028207	hsa-miR-4303	CLIP-seq
MIRT1103154	hsa-miR-4318	CLIP-seq
MIRT2028208	hsa-miR-4329	CLIP-seq
MIRT1103157	hsa-miR-4648	CLIP-seq
MIRT1103158	hsa-miR-4654	CLIP-seq
MIRT2028209	hsa-miR-4762-3p	CLIP-seq
MIRT1103163	hsa-miR-4769-5p	CLIP-seq
MIRT2028210	hsa-miR-502-5p	CLIP-seq
MIRT1103165	hsa-miR-521	CLIP-seq
MIRT1103166	hsa-miR-562	CLIP-seq
MIRT2028211	hsa-miR-580	CLIP-seq
MIRT2028212	hsa-miR-624	CLIP-seq
MIRT2438285	hsa-miR-3685	CLIP-seq
MIRT2438286	hsa-miR-384	CLIP-seq
MIRT2438287	hsa-miR-4659a-3p	CLIP-seq
MIRT2438288	hsa-miR-4659b-3p	CLIP-seq
MIRT2438289	hsa-miR-579	CLIP-seq

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000408	Component	EKC/KEOPS complex	IBA
GO:0000408	Component	EKC/KEOPS complex	IDA	27903914, 28805828, 31481669
GO:0005515	Function	Protein binding	IPI	25416956, 27903914, 28514442, 31481669, 32296183, 33961781
GO:0005634	Component	Nucleus	IDA	28805828
GO:0005634	Component	Nucleus	IEA
GO:0005654	Component	Nucleoplasm	IDA
GO:0005737	Component	Cytoplasm	IDA	28805828
GO:0005737	Component	Cytoplasm	IEA
GO:0008033	Process	TRNA processing	IEA
GO:0016604	Component	Nuclear body	IDA
GO:0070525	Process	TRNA threonylcarbamoyladenosine metabolic process	IBA

Other IDs

• MIM: 300060
• HGNC: 26058
• e!Ensembl: ENSG00000196976

Protein

• UniProt ID: Q14657
• Protein name: EKC/KEOPS complex subunit LAGE3 (L antigen family member 3) (Protein ESO-3) (Protein ITBA2)
• Protein function: Component of the EKC/KEOPS complex that is required for the formation of a threonylcarbamoyl group on adenosine at position 37 (t(6)A37) in tRNAs that read codons beginning with adenine (PubMed:22912744, PubMed:27903914). The complex is probably
• PDB: 6GWJ
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF09341	Pcc1	62 → 135	Transcription factor Pcc1	Family

• Tissue specificity: TISSUE SPECIFICITY: Ubiquitous. {ECO:0000269|PubMed:12384295, ECO:0000269|PubMed:8786131}.
• Sequence:

  MRDADADAGGGADGGDGRGGHSCRGGVDTAAAPAGGAPPAHAPGPGRDAASAARGSRMRP
  HIFTLSVPFPTPLEAEIAHGSLAPDAEPHQRVVGKDLTVSGRILVVRWKAEDCRLLRISV
  INFLDQLSLVVRTMQRFGPPVSR

• Sequence length: 143

Associated diseases

Causal
Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Galloway-Mowat syndrome 2, X-linked	Pathogenic	rs1557211306, rs1557211209, rs1557211410	RCV000513483 RCV000512681 RCV000513038

Unknown
Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
LAGE3-related disorder	Likely benign; Benign; Conflicting classifications of pathogenicity; Uncertain significance	rs781818854, rs782232215, rs782572582, rs782761326, rs2069248483, rs782309060, rs782065337, rs782228821, rs2069255659, rs1297949332, rs11538409, rs190210772, rs146063259, rs2276463	RCV003968638 RCV003941337 RCV003943731 RCV003906553 RCV003399625 RCV003394471 RCV003410902 RCV003414230 RCV003981831 RCV003981839 RCV003960845 RCV003977971 RCV003968185 RCV003902971

Associations from Text Mining
Disease Name	Relationship Type	References
Carcinoma Hepatocellular	Associate	35313850
Galloway Mowat syndrome	Associate	36755238
Hypothyroidism	Associate	36755238
Melanoma	Stimulate	33829062
Melanoma Cutaneous Malignant	Associate	33829062
Microcephaly	Associate	36755238
Neoplasms	Associate	35313850
Nephrosis congenital	Associate	37845138
Nephrotic Syndrome	Associate	36755238