RPL22

ribosomal protein L22, the group of L ribosomal proteins

Basic information

Region (hg38): 1:6185020-6209389

Links

ENSG00000116251 ∙ NCBI:6146 ∙ OMIM:180474 ∙ HGNC:10315 ∙ Uniprot:P35268 ∙ 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 RPL22 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RPL22 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						0
missense			3			3
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	3	0	0

Variants in RPL22

This is a list of pathogenic ClinVar variants found in the RPL22 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-6192969-C-G		not specified	Uncertain significance (Aug 08, 2022)
1-6197704-G-A		not specified	Uncertain significance (Jun 09, 2022)
1-6199569-G-A		not specified	Uncertain significance (Dec 20, 2022)
1-6206540-C-G		not specified	Uncertain significance (Aug 02, 2023)
1-6206609-G-A		not specified	Uncertain significance (Dec 13, 2023)
1-6206636-G-A		not specified	Uncertain significance (Oct 25, 2022)
1-6206652-C-G		not specified	Uncertain significance (Sep 23, 2023)
1-6206669-G-A		not specified	Uncertain significance (Dec 09, 2023)
1-6206671-G-A		not specified	Uncertain significance (Mar 02, 2023)
1-6206695-A-G		not specified	Uncertain significance (May 30, 2024)
1-6206714-G-A		not specified	Uncertain significance (Jun 24, 2022)
1-6207407-G-A		not specified	Uncertain significance (Apr 18, 2023)
1-6207408-G-A		not specified	Uncertain significance (Oct 21, 2021)
1-6207417-C-T		not specified	Uncertain significance (Feb 10, 2022)
1-6207444-T-C		not specified	Uncertain significance (Jul 14, 2023)
1-6207464-G-A		not specified	Uncertain significance (Feb 07, 2023)
1-6207477-G-C		not specified	Uncertain significance (Sep 23, 2023)
1-6208912-G-A		not specified	Uncertain significance (Nov 15, 2021)
1-6209160-T-G		not specified	Uncertain significance (Oct 10, 2023)
1-6209164-G-A			Likely benign (Dec 31, 2019)
1-6209287-G-A		not specified	Uncertain significance (Jan 24, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RPL22	protein_coding	protein_coding	ENST00000234875	4	28121

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.156	0.782	125737	0	4	125741	0.0000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.67	32	71.8	0.445	0.00000420	848
Missense in Polyphen		5	14.801	0.33781		227
Synonymous	0.129	27	27.9	0.969	0.00000189	219
Loss of Function	1.53	2	6.06	0.330	2.54e-7	84

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)	0.0000355	0.0000352
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: 0.280

Intolerance Scores

• rvis_EVS: 0.01
• rvis_percentile_EVS: 54.63

Haploinsufficiency Scores

• pHI: 0.352
• hipred: Y
• hipred_score: 0.842
• ghis: 0.658

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.982

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Low	Low	Low
Primary Immunodeficiency	Low	Low	Low
Cancer	Low	Low	Low

Mouse Genome Informatics

• Gene name: Rpl22
• Phenotype: hematopoietic system phenotype; normal phenotype; immune system phenotype; renal/urinary system phenotype; endocrine/exocrine gland phenotype; cellular phenotype

Zebrafish Information Network

• Gene name: rpl22
• Affected structure: alpha-beta T cell
• Phenotype tag: abnormal
• Phenotype quality: aplastic/hypoplastic

Gene ontology

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