RPL22L1

ribosomal protein L22 like 1, the group of L ribosomal proteins

Basic information

Region (hg38): 3:170864875-170870208

Links

ENSG00000163584 ∙ NCBI:200916 ∙ ∙ HGNC:27610 ∙ Uniprot:Q6P5R6 ∙ 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 RPL22L1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RPL22L1 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			5			5
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	5	0	0

Variants in RPL22L1

This is a list of pathogenic ClinVar variants found in the RPL22L1 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-170866390-G-A		not specified	Uncertain significance (Apr 18, 2023)
3-170866402-T-C		not specified	Uncertain significance (May 31, 2023)
3-170866429-C-A		not specified	Uncertain significance (Sep 21, 2023)
3-170868022-A-C		not specified	Uncertain significance (Nov 03, 2023)
3-170868066-A-C		not specified	Uncertain significance (Jul 09, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RPL22L1	protein_coding	protein_coding	ENST00000295830	4	5609

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00105	0.618	121010	0	7	121017	0.0000289

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.351	71	63.2	1.12	0.00000352	803
Missense in Polyphen		19	14.5	1.3103		253
Synonymous	-0.787	26	21.4	1.22	0.00000115	208
Loss of Function	0.557	5	6.54	0.765	3.37e-7	80

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000174	0.000169
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000294	0.0000275
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.000185	0.000169

dbNSFP

Source: dbNSFP

• Pathway: Ribosome - Homo sapiens (human);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: 0.106

Intolerance Scores

• rvis_EVS: 0.19
• rvis_percentile_EVS: 66.57

Haploinsufficiency Scores

• pHI: 0.154
• hipred: N
• hipred_score: 0.286
• ghis: 0.594

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: N
• gene_indispensability_score: 2.22e-16

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rpl22l1
• Phenotype: embryo phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span)

Zebrafish Information Network

• Gene name: rpl22l1
• Affected structure: gamma-delta T cell
• Phenotype tag: abnormal
• Phenotype quality: aplastic/hypoplastic

Gene ontology

• Biological process: translation
• Cellular component: cytosolic large ribosomal subunit
• Molecular function: RNA binding;structural constituent of ribosome