RPL11 (ribosomal protein L11)

Gene

• Entrez ID: 6135
• Gene name: Ribosomal protein L11
• Gene symbol: RPL11
• Synonyms (NCBI Gene): DBA7, GIG34, L11, uL5
• Chromosome: 1
• Chromosome location: 1p36.11
• Summary: Ribosomes, the organelles that catalyze protein synthesis, consist of a small 40S subunit and a large 60S subunit. Together these subunits are composed of 4 RNA species and approximately 80 structurally distinct proteins. This gene encodes a ribosomal pro

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs121434389	C>T	Pathogenic	Stop gained, coding sequence variant
rs151155897	G>A	Pathogenic	Splice acceptor variant
rs587777119	AA>-	Pathogenic	Coding sequence variant, frameshift variant
rs587777120	T>-	Pathogenic	Coding sequence variant, frameshift variant
rs886041528	->T	Pathogenic	Frameshift variant, coding sequence variant
rs1553121678	CTTCGCA>-	Pathogenic	Frameshift variant, coding sequence variant
rs1553121684	C>-	Pathogenic	Frameshift variant, coding sequence variant
rs1553121689	CT>-	Pathogenic	Frameshift variant, coding sequence variant
rs1553121795	G>A	Likely-pathogenic	Splice donor variant
rs1570566590	CT>-	Pathogenic	Frameshift variant, coding sequence variant
rs1570566592	GT>-	Pathogenic	Frameshift variant, coding sequence variant
rs1570566714	->CC	Likely-pathogenic	Frameshift variant, coding sequence variant
rs1570568289	->SVA	Pathogenic	Coding sequence variant, inframe indel
rs1570569083	AGG>-	Pathogenic	Inframe deletion, coding sequence variant
rs1570569383	A>G	Pathogenic	Splice acceptor variant

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT048974	hsa-miR-92a-3p	CLASH	23622248
MIRT037976	hsa-miR-505-5p	CLASH	23622248
MIRT1315853	hsa-miR-1261	CLIP-seq
MIRT1315854	hsa-miR-4420	CLIP-seq
MIRT1315855	hsa-miR-4681	CLIP-seq
MIRT1315856	hsa-miR-570	CLIP-seq
MIRT1315853	hsa-miR-1261	CLIP-seq
MIRT1315857	hsa-miR-137	CLIP-seq
MIRT1315854	hsa-miR-4420	CLIP-seq
MIRT1315856	hsa-miR-570	CLIP-seq

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000027	Process	Ribosomal large subunit assembly	IMP	24120868
GO:0002181	Process	Cytoplasmic translation	IC	23636399
GO:0002181	Process	Cytoplasmic translation	IDA	25957688
GO:0002181	Process	Cytoplasmic translation	NAS	25901680
GO:0003723	Function	RNA binding	HDA	22681889
GO:0003723	Function	RNA binding	IBA
GO:0003723	Function	RNA binding	IEA
GO:0003723	Function	RNA binding	TAS	7748210
GO:0003735	Function	Structural constituent of ribosome	IBA
GO:0003735	Function	Structural constituent of ribosome	IDA	23636399, 32669547
GO:0003735	Function	Structural constituent of ribosome	IEA
GO:0003735	Function	Structural constituent of ribosome	IMP	18697920
GO:0003735	Function	Structural constituent of ribosome	NAS	12962325
GO:0003735	Function	Structural constituent of ribosome	TAS	7748210
GO:0005515	Function	Protein binding	IPI	15195100, 15314173, 17110929, 17310983, 17373842, 17599065, 18274552, 18560357, 19417104, 19713960, 21145461, 21399665, 21988832, 23507139, 23776465, 24556985, 24965446, 25416956, 25910212, 27829214, 30021884, 32296183, 32814053, 33961781, 35271311
GO:0005634	Component	Nucleus	IEA
GO:0005654	Component	Nucleoplasm	IDA	23776465, 24120868
GO:0005730	Component	Nucleolus	HDA	16791210
GO:0005730	Component	Nucleolus	IDA	15195100, 23776465
GO:0005730	Component	Nucleolus	IEA
GO:0005737	Component	Cytoplasm	HDA	16791210
GO:0005737	Component	Cytoplasm	IDA	15314173, 24120868
GO:0005737	Component	Cytoplasm	IEA
GO:0005737	Component	Cytoplasm	NAS	25901680
GO:0005829	Component	Cytosol	TAS
GO:0005840	Component	Ribosome	IEA
GO:0006364	Process	RRNA processing	IMP	18697920
GO:0006412	Process	Translation	IBA
GO:0006412	Process	Translation	IEA
GO:0006412	Process	Translation	NAS	12962325
GO:0006412	Process	Translation	TAS	7748210
GO:0006605	Process	Protein targeting	IMP	15195100
GO:0008097	Function	5S rRNA binding	IMP	18560357
GO:0010628	Process	Positive regulation of gene expression	IDA	18560357
GO:0016020	Component	Membrane	HDA	19946888
GO:0019843	Function	RRNA binding	IEA
GO:0022625	Component	Cytosolic large ribosomal subunit	HDA	12962325
GO:0022625	Component	Cytosolic large ribosomal subunit	IBA
GO:0022625	Component	Cytosolic large ribosomal subunit	IDA	25957688, 32669547
GO:0022625	Component	Cytosolic large ribosomal subunit	IEA
GO:0022625	Component	Cytosolic large ribosomal subunit	IPI	25901680
GO:0022625	Component	Cytosolic large ribosomal subunit	TAS	7748210
GO:0022626	Component	Cytosolic ribosome	IDA	23636399
GO:0031625	Function	Ubiquitin protein ligase binding	IPI	18560357
GO:0032092	Process	Positive regulation of protein binding	IMP	18560357
GO:0032435	Process	Negative regulation of proteasomal ubiquitin-dependent protein catabolic process	IEA
GO:0032435	Process	Negative regulation of proteasomal ubiquitin-dependent protein catabolic process	ISS
GO:0032991	Component	Protein-containing complex	IDA	15314173
GO:0034504	Process	Protein localization to nucleus	IEA
GO:0034504	Process	Protein localization to nucleus	ISS
GO:0042273	Process	Ribosomal large subunit biogenesis	IMP	18697920
GO:0050821	Process	Protein stabilization	IMP	18560357
GO:0070062	Component	Extracellular exosome	HDA	20458337
GO:1901796	Process	Regulation of signal transduction by p53 class mediator	IMP	24120868
GO:1901798	Process	Positive regulation of signal transduction by p53 class mediator	IEA
GO:1904667	Process	Negative regulation of ubiquitin protein ligase activity	IMP	18560357
GO:1990904	Component	Ribonucleoprotein complex	IEA
GO:1990948	Function	Ubiquitin ligase inhibitor activity	IMP	18560357
GO:2000059	Process	Negative regulation of ubiquitin-dependent protein catabolic process	IMP	18560357
GO:2000435	Process	Negative regulation of protein neddylation	IDA	18560357

Other IDs

• MIM: 604175
• HGNC: 10301
• e!Ensembl: ENSG00000142676

Protein

• UniProt ID: P62913
• Protein name: Large ribosomal subunit protein uL5 (60S ribosomal protein L11) (CLL-associated antigen KW-12)
• Protein function: Component of the ribosome, a large ribonucleoprotein complex responsible for the synthesis of proteins in the cell (PubMed:19191325, PubMed:32669547). The small ribosomal subunit (SSU) binds messenger RNAs (mRNAs) and translates the encoded mess
• PDB: 4UG0, 4V6X, 4XXB, 5AJ0, 5LKS, 5T2C, 6IP5, 6IP6, 6IP8, 6LQM, 6LSR, 6LSS, 6LU8, 6OLE, 6OLF, 6OLG, 6OLI, 6OLZ, 6OM0, 6OM7, 6QZP, 6W6L, 6XA1, 6Y0G, 6Y2L, 6Y57, 6Y6X, 6Z6L, 6Z6M, 6Z6N, 6ZM7, 6ZME, 6ZMI, 6ZMO, 7BHP, 7F5S, 7OW7, 7QVP, 7XNX, 7XNY, 8A3D, 8BGU, 8FL0, 8FL2, 8FL3, 8FL4, 8FL6, 8FL7, 8FL9, 8FLA, 8FLB
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF00281	Ribosomal_L5	10 → 63	Ribosomal protein L5	Domain
  PF00673	Ribosomal_L5_C	67 → 165	ribosomal L5P family C-terminus	Domain

• Sequence:

  MAQDQGEKENPMRELRIRKLCLNICVGESGDRLTRAAKVLEQLTGQTPVFSKARYTVRSF
  GIRRNEKIAVHCTVRGAKAEEILEKGLKVREYELRKNNFSDTGNFGFGIQEHIDLGIKYD
  PSIGIYGLDFYVVLGRPGFSIADKKRRTGCIGAKHRISKEEAMRWFQQKYDGIILPGK

• Sequence length: 178

Pathways

KEGG:

Ribosome
Coronavirus disease - COVID-19

Reactome:

L13a-mediated translational silencing of Ceruloplasmin expression
SRP-dependent cotranslational protein targeting to membrane
Viral mRNA Translation
Major pathway of rRNA processing in the nucleolus and cytosol
Formation of a pool of free 40S subunits
GTP hydrolysis and joining of the 60S ribosomal subunit
Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC)
Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC)

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
Anemia	Likely pathogenic	rs1570566714	RCV001003786	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Diamond-Blackfan anemia	Pathogenic; Likely pathogenic	rs2124429127, rs2124429140, rs2124432051, rs2124429146, rs2124430919, rs2124429183, rs2523394868, rs2523400126, rs2523391493, rs2523403053, rs2523404237, rs2523395126, rs151155897, rs2523398100, rs2523400044, rs2523395100, rs121434389, rs1570566590, rs2523395112, rs2523400065, rs2523400088, rs1553121795, rs1553121684, rs1570566592, rs1570569383, rs1644516691, rs1644530053	RCV001388016 RCV001381985 RCV002359168 RCV001966162 RCV001989229 RCV001934782 RCV002452034 RCV002326146 RCV002358008 RCV002330453 RCV002335895 RCV002383415 RCV002405819 RCV002405831 RCV002442210 RCV002829097 RCV000695992 RCV002354149 RCV001216188 RCV003508817 RCV003616483 RCV003616627 RCV000638825 RCV000638828 RCV000796614 RCV000792669 RCV001062578 RCV002339708	★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Diamond-Blackfan anemia 7	Pathogenic; Likely pathogenic	rs587777119, rs587777120, rs2523395201, rs2523395096, rs2523391493, rs121434389, rs1570566590, rs151155897, rs2523395104, rs1553121689, rs1553121678, rs1644530053	RCV000087040 RCV000087041 RCV002283845 RCV002287313 RCV005635519 RCV000006107 RCV000006108 RCV000006110 RCV003142524 RCV005869583 RCV000625833 RCV001283765	★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Reticulocytopenia	Likely pathogenic	rs1570566714	RCV001003786	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
RPL11-related disorder	Pathogenic	rs1570566590	RCV003415663	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)

Unknown / Other Associations
Phenotype Name	Clinical Significance	Source	Evidence Score
ANEMIA, DIAMOND-BLACKFAN	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Familial cancer of breast	Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Hepatocellular carcinoma	Conflicting classifications of pathogenicity	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
PROSTATIC NEOPLASMS	—	CTD	★★☆☆☆ 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	Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Associations from Text Mining
Disease Name	Relationship Type	References	Evidence Score
Alzheimer Disease	Associate	35766008, 38176923	★☆☆☆☆ Found in Text Mining only
Anemia Diamond Blackfan	Associate	19061985, 19765279, 19773262, 20116044, 20378560, 20960466, 22431104, 22689679, 24463277, 24675553, 25946618, 30700418, 33862179, 35038319, 36735910	★☆☆☆☆ Found in Text Mining only
Bone Diseases Developmental	Associate	28595297	★☆☆☆☆ Found in Text Mining only
Breast Neoplasms	Associate	29081411, 33305312, 36984424	★☆☆☆☆ Found in Text Mining only
Capillary Malformation Arteriovenous Malformation	Associate	19773262, 20960466	★☆☆☆☆ Found in Text Mining only
Carcinoma Hepatocellular	Associate	32316188, 34433556	★☆☆☆☆ Found in Text Mining only
Carcinoma Non Small Cell Lung	Associate	36869281	★☆☆☆☆ Found in Text Mining only
Cleft Palate	Associate	19061985	★☆☆☆☆ Found in Text Mining only
COVID 19	Associate	36856850	★☆☆☆☆ Found in Text Mining only
Diabetic Retinopathy	Associate	35154512	★☆☆☆☆ Found in Text Mining only
Ectrodactyly	Associate	19773262	★☆☆☆☆ Found in Text Mining only
Inflammation	Associate	35154512	★☆☆☆☆ Found in Text Mining only
Microphthalmia Isolated 1	Associate	19061985	★☆☆☆☆ Found in Text Mining only
Nasopharyngeal Carcinoma	Associate	36107539	★☆☆☆☆ Found in Text Mining only
Neoplasms	Associate	14612427, 20221446, 23671674, 26220995, 36869281	★☆☆☆☆ Found in Text Mining only
Neoplasms	Inhibit	24061479	★☆☆☆☆ Found in Text Mining only
Pigmentary Disorder Reticulate with Systemic Manifestations	Associate	35154512	★☆☆☆☆ Found in Text Mining only
Stomach Neoplasms	Associate	24045667	★☆☆☆☆ Found in Text Mining only
Thumb deformity	Associate	19061985	★☆☆☆☆ Found in Text Mining only
Triple Negative Breast Neoplasms	Associate	33305312	★☆☆☆☆ Found in Text Mining only