RPL9

ribosomal protein L9, the group of L ribosomal proteins

Basic information

Region (hg38): 4:39452587-39458931

Links

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

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

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

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.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous			1	13	1	15
missense			21			21
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region			1	4	1	6
non coding				17	12	29
Total	0	0	22	30	13

Variants in RPL9

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

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
4-39454544-T-C			Likely benign (Oct 29, 2023)
4-39454547-T-C		not specified	Uncertain significance (Sep 22, 2023)
4-39454552-A-G			Likely benign (Feb 09, 2023)
4-39454554-C-A		not specified	Uncertain significance (Aug 04, 2023)
4-39454558-C-A		not specified	Uncertain significance (Sep 06, 2024)
4-39454585-G-T			Likely benign (Dec 07, 2024)
4-39454615-G-C		not specified	Uncertain significance (Jan 10, 2025)
4-39454619-T-C		not specified	Uncertain significance (Jan 18, 2025)
4-39454631-G-A			Uncertain significance (Sep 29, 2024)
4-39454652-A-T			Uncertain significance (Aug 04, 2024)
4-39454658-G-A			Likely benign (Aug 23, 2022)
4-39454772-G-A			Benign (May 14, 2021)
4-39454848-T-C			Likely benign (Dec 09, 2023)
4-39454874-A-C			Likely benign (Sep 21, 2023)
4-39454884-A-G			Uncertain significance (Oct 21, 2024)
4-39454906-A-T			Uncertain significance (May 10, 2024)
4-39454913-T-C			Likely benign (Nov 19, 2024)
4-39454922-T-C			Likely benign (Apr 14, 2023)
4-39454922-T-G			Uncertain significance (Jul 16, 2022)
4-39454931-T-C			Likely benign (Jan 29, 2025)
4-39454955-A-G			Likely benign (Apr 25, 2024)
4-39454956-G-A			Likely benign (Jul 28, 2023)
4-39455015-T-C			Benign (May 14, 2021)
4-39456237-T-C			Benign (May 14, 2021)
4-39456250-T-TG			Benign (May 14, 2021)

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