RPL9

ribosomal protein L9, the group of L ribosomal proteins

Basic information

Region (hg38): 4:39452586-39458931

Links

ENSG00000163682 ∙ NCBI:6133 ∙ OMIM:603686 ∙ HGNC:10369 ∙ Uniprot:P32969 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the RPL9 gene.

• not provided (32 variants)
• Inborn genetic diseases (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RPL9 gene is commonly pathogenic or not.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				3	1	4
missense			10			10
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice variant				2	1	3
non coding				6	12	18
Total	0	0	10	11	14

Variants in RPL9

This is a list of pathogenic ClinVar variants found in the RPL9 region.

Position	Type	Phenotype	Significance	ClinVar
4-39454554-C-A		Inborn genetic diseases	Uncertain significance (Mar 02, 2023)
4-39454558-C-A		Inborn genetic diseases	Uncertain significance (Jan 26, 2023)
4-39454631-G-A			Uncertain significance (Jun 08, 2022)
4-39454658-G-A			Likely benign (Aug 23, 2022)
4-39454772-G-A			Benign (May 14, 2021)
4-39454922-T-G			Uncertain significance (Jul 16, 2022)
4-39454931-T-C			Likely benign (Oct 18, 2022)
4-39455015-T-C			Benign (May 14, 2021)
4-39456237-T-C			Benign (May 14, 2021)
4-39456250-T-TG			Benign (May 14, 2021)
4-39456390-G-A			Likely benign (Jul 21, 2022)
4-39456390-G-C			Benign (Nov 01, 2022)
4-39456422-C-G			Uncertain significance (Jul 17, 2022)
4-39456431-A-G			Benign (Nov 03, 2022)
4-39456462-A-G		Inborn genetic diseases	Uncertain significance (Jul 13, 2022)
4-39456514-C-G			Uncertain significance (Sep 30, 2022)
4-39456532-G-A		Inborn genetic diseases	Uncertain significance (Oct 04, 2022)
4-39456544-TTAAA-T			Benign (Nov 02, 2022)
4-39456552-A-G			Likely benign (May 21, 2022)
4-39457411-T-C			Benign (May 15, 2021)
4-39457534-G-A			Benign (May 14, 2021)
4-39457570-T-C			Likely benign (Oct 19, 2022)
4-39457625-A-G			Likely benign (Jul 08, 2022)
4-39457637-G-A			Likely benign (Sep 09, 2022)
4-39457677-C-T		Inborn genetic diseases	Uncertain significance (Mar 11, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RPL9	protein_coding	protein_coding	ENST00000449470	6	4825

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.962	0.0380	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.59	62	109	0.571	0.00000574	1254
Missense in Polyphen		5	13.32	0.37537		199
Synonymous	-1.60	47	35.0	1.34	0.00000166	358
Loss of Function	2.96	0	10.2	0.00	5.16e-7	121

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Pathway: Ribosome - Homo sapiens (human);Cytoplasmic Ribosomal Proteins;SRP-dependent cotranslational protein targeting to membrane;Eukaryotic Translation Initiation;Eukaryotic Translation Termination;Translation;Selenocysteine synthesis;Metabolism of proteins;Metabolism of amino acids and derivatives;Metabolism of RNA;Formation of a pool of free 40S subunits;Metabolism;Nonsense-Mediated Decay (NMD);Selenoamino acid metabolism;Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC);Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC);L13a-mediated translational silencing of Ceruloplasmin expression;Peptide chain elongation;Eukaryotic Translation Elongation;GTP hydrolysis and joining of the 60S ribosomal subunit;Cap-dependent Translation Initiation (Consensus)

Recessive Scores

• pRec: 0.107

Intolerance Scores

• rvis_EVS: -0.16
• rvis_percentile_EVS: 41.25

Haploinsufficiency Scores

• pHI: 0.993
• hipred: Y
• hipred_score: 0.802
• ghis: 0.473

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.897

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Rpl9

Zebrafish Information Network

• Gene name: rpl9
• Affected structure: head
• Phenotype tag: abnormal
• Phenotype quality: decreased size

Gene ontology

• Biological process: nuclear-transcribed mRNA catabolic process, nonsense-mediated decay;cytoplasmic translation;translation;translational initiation;SRP-dependent cotranslational protein targeting to membrane
• Cellular component: nucleus;cytosol;ribosome;focal adhesion;membrane;cytosolic large ribosomal subunit
• Molecular function: RNA binding;structural constituent of ribosome;protein binding;rRNA binding