Gene Details | GeDiPNet - Complete Gene Info, Disease Associations & Pathways

Gene Gene information from NCBI Gene database. Gene SNPs miRNA Gene ontology Other IDs Protein Associated diseases
Entrez ID	8270
Gene name	L antigen family member 3
Gene symbol	LAGE3
Synonyms (NCBI Gene)	CVG5DXS9879EDXS9951EESO3GAMOS2ITBA2Pcc1
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

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

Show/Hide all (41)

miRTarBase ID	miRNA	Experiments
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

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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

MIM	HGNC	e!Ensembl
300060	26058	ENSG00000196976

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

Interactions

View interactions

Evidence Score: ★☆☆☆☆ Gene-disease association found in Text Mining only ★★☆☆☆ Found in Text Mining and Unknown/Other Associations ★★★☆☆ Reported in Unknown/Other Associations across ≥2 Sources ★★★★☆ ClinVar: Pathogenic/Likely Pathogenic (<5 Variants) ★★★★★ ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)

Show/Hide Causal Diseases (1)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Galloway-Mowat syndrome 2, X-linked	Pathogenic	rs1557211306, rs1557211209, rs1557211410	RCV000513483 RCV000512681 RCV000513038	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)

Show/Hide Unknown Diseases (3)

Phenotype Name	Clinical Significance	Source	Evidence Score
Unknown / Other Associations ClinVar entries with uncertain/conflicting evidence, and associations from other databases (OMIM, Orphanet, GWAS, etc.) where the gene is not established as causal.
GALLOWAY MOWAT SYNDROME	—	CTD, Disgenet CTD, Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
GALLOWAY-MOWAT SYNDROME	—	CTD, Orphanet CTD, Orphanet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
LAGE3-related disorder	Likely benign; Benign; Conflicting classifications of pathogenicity; Uncertain significance	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Show/Hide Text Mining Associations (41)

Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Associations from Text Mining Disease associations identified through text mining
Aqueductal Stenosis	Aqueductal Stenosis	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Arachnodactyly	Arachnodactyly	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Byzanthine arch palate	High palate	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Carcinoma Hepatocellular	Hepatocellular carcinoma	Pubtator	35313850	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Cerebellar atrophy	Cerebellar atrophy	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Cerebral atrophy	Cerebral Atrophy	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Dwarfism	Dwarfism	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Esotropia	Esotropia	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Galloway Mowat syndrome	Galloway-Mowat Syndrome	BEFREE	28805828, 30141175		★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Galloway Mowat syndrome	Galloway-Mowat Syndrome	ORPHANET_DG	28805828		★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Galloway Mowat syndrome	Galloway-Mowat Syndrome	CTD_human_DG	28805828		★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Galloway Mowat syndrome	Galloway-mowat syndrome	Pubtator	36755238	Associate	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Galloway-Mowat syndrome	Galloway-Mowat Syndrome	Orphanet			★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
GALLOWAY-MOWAT SYNDROME 2, X-LINKED	Galloway-Mowat Syndrome	GENOMICS_ENGLAND_DG	28805828		★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
GALLOWAY-MOWAT SYNDROME 2, X-LINKED	Galloway-Mowat Syndrome	UNIPROT_DG	28805828		★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
GALLOWAY-MOWAT SYNDROME 2, X-LINKED	Galloway-Mowat Syndrome	CLINVAR_DG			★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Global developmental delay	Developmental Delay	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Glomerulonephritis	Glomerulonephritis	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Glomerulonephritis, Minimal Change	Glomerulonephritis	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Glomerulosclerosis (disorder)	Glomerulosclerosis	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Hemiplegia/hemiparesis	Hemiplegia/hemiparesis	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Hiatal Hernia	Hiatal Hernia	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Hypothyroidism	Hypothyroidism	Pubtator	36755238	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Impaired cognition	Impaired Cognition	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Intellectual Disability	Mental retardation	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Kidney Diseases	Kidney Disease	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Macrotia	Macrotia	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Melanoma	Melanoma	Pubtator	33829062	Stimulate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Melanoma Cutaneous Malignant	Melanoma	Pubtator	33829062	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Microcephaly	Microcephaly	BEFREE	30141175		★★★★★ ★☆☆☆☆ Found in Text Mining only
Microcephaly	Microcephaly	Pubtator	36755238	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Microcephaly	Microcephaly	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Micrognathism	Micrognathism	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Nephrosis congenital	Nephrotic syndrome	Pubtator	37845138	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Nephrotic Syndrome	Nephrotic syndrome	Pubtator	36755238	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Nephrotic Syndrome	Nephrotic Syndrome	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Nystagmus	Nystagmus	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Pachygyria	Pachygyria	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Polymicrogyria	Polymicrogyria	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Scoliosis, unspecified	Scoliosis	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Steroid resistant nephrotic syndrome of childhood	Steroid resistant nephrotic syndrome	BEFREE	30141175		★★★★★ ★☆☆☆☆ Found in Text Mining only