LAS1L (LAS1 like ribosome biogenesis factor)

Gene

• Entrez ID: 81887
• Gene name: LAS1 like ribosome biogenesis factor
• Gene symbol: LAS1L
• Synonyms (NCBI Gene): Las1, Las1-like, MRXSWTS, WTS, dJ475B7.2
• Chromosome: X
• Chromosome location: Xq12

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs797044926	C>T	Likely-pathogenic	Missense variant, non coding transcript variant, coding sequence variant
rs1057518699	G>A	Likely-pathogenic	Missense variant, coding sequence variant, non coding transcript variant
rs1057522039	G>A	Likely-pathogenic	Coding sequence variant, stop gained, genic downstream transcript variant, non coding transcript variant
rs1602612611	C>T	Likely-pathogenic	Coding sequence variant, non coding transcript variant, missense variant

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT022244	hsa-miR-124-3p	Proteomics;Microarray	18668037
MIRT051007	hsa-miR-17-5p	CLASH	23622248
MIRT1104955	hsa-miR-181a	CLIP-seq
MIRT1104956	hsa-miR-181b	CLIP-seq
MIRT1104957	hsa-miR-181c	CLIP-seq
MIRT1104958	hsa-miR-181d	CLIP-seq
MIRT1104959	hsa-miR-219-1-3p	CLIP-seq
MIRT1104960	hsa-miR-3138	CLIP-seq
MIRT1104961	hsa-miR-3165	CLIP-seq
MIRT1104962	hsa-miR-331-3p	CLIP-seq
MIRT1104963	hsa-miR-3617	CLIP-seq
MIRT1104964	hsa-miR-4262	CLIP-seq
MIRT1104965	hsa-miR-4474-3p	CLIP-seq
MIRT1104966	hsa-miR-4645-5p	CLIP-seq
MIRT1104967	hsa-miR-4673	CLIP-seq
MIRT1104968	hsa-miR-4682	CLIP-seq
MIRT1104969	hsa-miR-4698	CLIP-seq
MIRT1104970	hsa-miR-549	CLIP-seq
MIRT1104971	hsa-miR-571	CLIP-seq
MIRT1104972	hsa-miR-640	CLIP-seq
MIRT1104973	hsa-miR-641	CLIP-seq
MIRT1550670	hsa-miR-150	CLIP-seq
MIRT1550671	hsa-miR-1915	CLIP-seq
MIRT1104966	hsa-miR-4645-5p	CLIP-seq
MIRT1104967	hsa-miR-4673	CLIP-seq
MIRT1550672	hsa-miR-4713-5p	CLIP-seq
MIRT1550673	hsa-miR-4726-3p	CLIP-seq
MIRT1550674	hsa-miR-532-3p	CLIP-seq
MIRT1550675	hsa-miR-626	CLIP-seq
MIRT1104972	hsa-miR-640	CLIP-seq
MIRT1104960	hsa-miR-3138	CLIP-seq
MIRT1104961	hsa-miR-3165	CLIP-seq
MIRT1104962	hsa-miR-331-3p	CLIP-seq
MIRT1104970	hsa-miR-549	CLIP-seq
MIRT1104972	hsa-miR-640	CLIP-seq
MIRT1104955	hsa-miR-181a	CLIP-seq
MIRT1104956	hsa-miR-181b	CLIP-seq
MIRT1104957	hsa-miR-181c	CLIP-seq
MIRT1104958	hsa-miR-181d	CLIP-seq
MIRT1104962	hsa-miR-331-3p	CLIP-seq
MIRT1104963	hsa-miR-3617	CLIP-seq
MIRT1104964	hsa-miR-4262	CLIP-seq
MIRT1104969	hsa-miR-4698	CLIP-seq
MIRT1104973	hsa-miR-641	CLIP-seq

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000460	Process	Maturation of 5.8S rRNA	IBA
GO:0000470	Process	Maturation of LSU-rRNA	IBA
GO:0003723	Function	RNA binding	HDA	22658674, 22681889
GO:0004519	Function	Endonuclease activity	IEA
GO:0005515	Function	Protein binding	IPI	22046132, 31288032
GO:0005634	Component	Nucleus	IBA
GO:0005634	Component	Nucleus	IEA
GO:0005654	Component	Nucleoplasm	IEA
GO:0005654	Component	Nucleoplasm	TAS
GO:0005730	Component	Nucleolus	IDA	31288032
GO:0005730	Component	Nucleolus	IEA
GO:0005737	Component	Cytoplasm	IEA
GO:0006364	Process	RRNA processing	IDA	22083961
GO:0006364	Process	RRNA processing	IEA
GO:0016020	Component	Membrane	HDA	19946888
GO:0016787	Function	Hydrolase activity	IEA
GO:0071339	Component	MLL1 complex	IDA
GO:0090730	Component	Las1 complex	IEA

Other IDs

• MIM: 300964
• HGNC: 25726
• e!Ensembl: ENSG00000001497

Protein

• UniProt ID: Q9Y4W2
• Protein name: Ribosomal biogenesis protein LAS1L (Endoribonuclease LAS1L) (EC 3.1.-.-) (Protein LAS1 homolog)
• Protein function: Required for the synthesis of the 60S ribosomal subunit and maturation of the 28S rRNA (PubMed:20647540). Functions as a component of the Five Friends of Methylated CHTOP (5FMC) complex; the 5FMC complex is recruited to ZNF148 by methylated CHTO
• PDB: 8FL2, 8FL3, 8FL4
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF04031	Las1	43 → 187	Las1-like	Family

• Sequence:

  MSWESGAGPGLGSQGMDLVWSAWYGKCVKGKGSLPLSAHGIVVAWLSRAEWDQVTVYLFC
  DDHKLQRYALNRITVWRSRSGNELPLAVASTADLIRCKLLDVTGGLGTDELRLLYGMALV
  RFVNLISERKTKFAKVPLKCLAQEVNIPDWIVDLRHELTHKKMPHINDCRRGCYFVLDWL
  QKTYWCRQLENSLRETWELEEFREGIEEEDQEEDKNIVVDDITEQKPEPQDDGKSTESDV
  KADGDSKGSEEVDSHCKKALSHKELYERARELLVSYEEEQFTVLEKFRYLPKAIKAWNNP
  SPRVECVLAELKGVTCENREAVLDAFLDDGFLVPTFEQLAALQIEYEDGQTEVQRGEGTD
  PKSHKNVDLNDVLVPKPFSQFWQPLLRGLHSQNFTQALLERMLSELPALGISGIRPTYIL
  RWTVELIVANTKTGRNARRFSAGQWEARRGWRLFNCSASLDWPRMVESCLGSPCWASPQL
  LRIIFKAMGQGLPDEEQEKLLRICSIYTQSGENSLVQEGSEASPIGKSPYTLDSLYWSVK
  PASSSFGSEAKAQQQEEQGSVNDVKEEEKEEKEVLPDQVEEEEENDDQEEEEEDEDDEDD
  EEEDRMEVGPFSTGQESPTAENARLLAQKRGALQGSAWQVSSEDVRWDTFPLGRMPGQTE
  DPAELMLENYDTMYLLDQPVLEQRLEPSTCKTDTLGLSCGVGSGNCSNSSSSNFEGLLWS
  QGQLHGLKTGLQLF

• Sequence length: 734

Pathways

Reactome:

Major pathway of rRNA processing in the nucleolus and cytosol

Associated diseases

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)

Causal
Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
Global developmental delay	Likely pathogenic; Pathogenic	rs1057518699	RCV000415340	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Wilson-Turner syndrome	Pathogenic; Likely pathogenic	rs1173514495, rs1057518699, rs1602612611	RCV000239552 RCV000239589 RCV000824689	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)

Unknown / Other Associations
Phenotype Name	Clinical Significance	Source	Evidence Score
Autism spectrum disorder	Uncertain significance	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
AUTISM SPECTRUM DISORDERS	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
HYPOGONADISM	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
INSOMNIA	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
INTELLECTUAL DEVELOPMENTAL DISORDER, X-LINKED, SYNDROMIC, WILSON-TURNER TYPE	—	Disgenet, HPO Disgenet, HPO	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Intellectual disability	Conflicting classifications of pathogenicity; Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
LAS1L-related disorder	Benign; Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Neurodevelopmental disorder	Uncertain significance	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
NEURODEVELOPMENTAL DISORDERS	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
PARTINGTON SYNDROME	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SPINAL MUSCULAR ATROPHY WITH RESPIRATORY DISTRESS TYPE 2	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Thyroid cancer, nonmedullary, 1	Uncertain significance	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Uterine corpus endometrial carcinoma	Uncertain significance	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
WILSON-TURNER X-LINKED MENTAL RETARDATION SYNDROME	—	CTD	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
X-LINKED SYNDROMIC INTELLECTUAL DISABILITY	—	ClinGen, GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Associations from Text Mining
Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Autism Spectrum Disorder	Autism	Pubtator	32193494	Associate	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Beta ketothiolase deficiency	Beta-ketothiolase deficiency	Pubtator	35627110	Associate	★☆☆☆☆ Found in Text Mining only
Brachycephaly	Brachycephaly	HPO_DG			★☆☆☆☆ Found in Text Mining only
Carcinogenesis	Carcinogenesis	Pubtator	18227151	Associate	★☆☆☆☆ Found in Text Mining only
Colorectal Carcinoma	Colorectal Cancer	UNIPROT_DG			★☆☆☆☆ Found in Text Mining only
Congenital small ears	Microtia	HPO_DG			★☆☆☆☆ Found in Text Mining only
Cryptorchidism	Cryptorchidism	HPO_DG			★☆☆☆☆ Found in Text Mining only
Dwarfism	Dwarfism	HPO_DG			★☆☆☆☆ Found in Text Mining only
Global developmental delay	Developmental Delay	CLINVAR_DG	25644381		★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Global developmental delay	Developmental Delay	HPO_DG			★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Gynecomastia	Gynecomastia	HPO_DG			★☆☆☆☆ Found in Text Mining only
Hypertrophy	Hypertrophy	Pubtator	18227151	Associate	★☆☆☆☆ Found in Text Mining only
Hypogonadism	Hypogonadism	HPO_DG			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Hypogonadotropic hypogonadism	Hypogonadotropic Hypogonadism	HPO_DG			★☆☆☆☆ Found in Text Mining only
Intellectual Disability	Mental retardation	GENOMICS_ENGLAND_DG	25644381		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Intellectual Disability	Mental retardation	BEFREE	28652339, 31288032		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Intellectual Disability	Intellectual developmental disorder	Pubtator	31288032	Associate	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Intellectual Disability	Mental retardation	HPO_DG			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Lung Neoplasms	Lung Neoplasms	BEFREE	14583591		★☆☆☆☆ Found in Text Mining only
Lung Neoplasms	Lung neoplasms	Pubtator	24682895	Associate	★☆☆☆☆ Found in Text Mining only
Lymphatic Metastasis	Lymphatic metastasis	Pubtator	24682895	Associate	★☆☆☆☆ Found in Text Mining only
Microcephaly	Microcephaly	HPO_DG			★☆☆☆☆ Found in Text Mining only
Micrognathism	Micrognathism	HPO_DG			★☆☆☆☆ Found in Text Mining only
Mood swings	Mood swings	HPO_DG			★☆☆☆☆ Found in Text Mining only
Motor Neuron Disease	Motor Neuron Disease	BEFREE	28652339, 31288032		★☆☆☆☆ Found in Text Mining only
Motor Neuron Disease	Motor neuron disease	Pubtator	31288032	Associate	★☆☆☆☆ Found in Text Mining only
Obesity	Obesity	HPO_DG			★☆☆☆☆ Found in Text Mining only
Penis agenesis	Penis Agenesis	HPO_DG			★☆☆☆☆ Found in Text Mining only
Specific learning disability	Specific Learning Disorder	HPO_DG			★☆☆☆☆ Found in Text Mining only
SPINAL MUSCULAR ATROPHY WITH RESPIRATORY DISTRESS 1	SPINAL MUSCULAR ATROPHY WITH RESPIRATORY DISTRESS	BEFREE	24647030		★☆☆☆☆ Found in Text Mining only
Spinal muscular atrophy with respiratory distress 1	Spinal muscular atrophy	Pubtator	35627110	Associate	★☆☆☆☆ Found in Text Mining only
Spinal muscular atrophy with respiratory distress type 2	Spinal Muscular Atrophy With Respiratory Distress	ORPHANET_DG	24647030		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Spinal muscular atrophy with respiratory distress type 2	Spinal Muscular Atrophy With Respiratory Distress	Orphanet			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Wilson-Turner syndrome	Wilson-Turner Syndrome	Orphanet			★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
WILSON-TURNER X-LINKED MENTAL RETARDATION SYNDROME	Mental Retardation, X-Linked	UNIPROT_DG	25644381		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
WILSON-TURNER X-LINKED MENTAL RETARDATION SYNDROME	Mental Retardation, X-Linked	ORPHANET_DG	25644381		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
WILSON-TURNER X-LINKED MENTAL RETARDATION SYNDROME	Mental Retardation, X-Linked	GENOMICS_ENGLAND_DG	26358559		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
WILSON-TURNER X-LINKED MENTAL RETARDATION SYNDROME	Mental Retardation, X-Linked	CTD_human_DG			★★☆☆☆ Found in Text Mining + Unknown/Other Associations