RPL28

ribosomal protein L28, the group of L ribosomal proteins|MicroRNA protein coding host genes

Basic information

Region (hg38): 19:55385931-55403250

Links

ENSG00000108107 ∙ NCBI:6158 ∙ OMIM:603638 ∙ HGNC:10330 ∙ Uniprot:P46779 ∙ 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 RPL28 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RPL28 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			4			4
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			2	1	1	4
Total	0	0	6	1	1

Variants in RPL28

This is a list of pathogenic ClinVar variants found in the RPL28 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-55386389-G-A		not specified	Uncertain significance (Jan 26, 2022)
19-55386595-A-G		not specified	Uncertain significance (Dec 19, 2022)
19-55386622-A-G		not specified	Uncertain significance (Mar 31, 2023)
19-55388016-C-T		not specified	Uncertain significance (Aug 28, 2023)
19-55391581-C-T		not specified	Uncertain significance (Aug 17, 2021)
19-55391634-T-C			Benign (Apr 10, 2018)
19-55391665-G-A		not specified	Likely benign (Nov 15, 2021)
19-55391735-C-A		not specified	Uncertain significance (Sep 26, 2023)
19-55401446-C-T		not specified	Uncertain significance (Jan 26, 2022)
19-55401453-C-A		not specified	Uncertain significance (Jun 03, 2022)
19-55401481-C-T		not specified	Likely benign (Jan 04, 2024)
19-55401541-C-T			Benign (Jul 20, 2018)
19-55401545-C-A		not specified	Uncertain significance (Jun 03, 2022)
19-55401545-C-T		not specified	Uncertain significance (Mar 01, 2024)
19-55401564-C-T		not specified	Uncertain significance (May 03, 2023)
19-55401578-T-G			Benign (Dec 31, 2019)
19-55401601-A-C			Likely benign (Jul 02, 2018)
19-55401603-C-T		not specified	Uncertain significance (Apr 25, 2022)
19-55401610-G-A			Benign (Jun 14, 2018)
19-55401618-C-T		not specified	Uncertain significance (Apr 07, 2023)
19-55401633-C-T		not specified	Uncertain significance (Dec 14, 2023)
19-55401660-G-T		not specified	Uncertain significance (Jul 05, 2023)
19-55401729-C-T		not specified	Uncertain significance (Dec 28, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RPL28	protein_coding	protein_coding	ENST00000558815	4	17900

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.769	0.224	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0677	101	103	0.981	0.00000609	1086
Missense in Polyphen		23	22.222	1.035		321
Synonymous	-1.19	49	39.5	1.24	0.00000204	343
Loss of Function	2.04	0	4.85	0.00	2.04e-7	61

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

• Function: FUNCTION: Component of the large ribosomal subunit. {ECO:0000305|PubMed:12962325}.
• 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: 0.221

Intolerance Scores

• rvis_EVS: 0.08
• rvis_percentile_EVS: 60.31

Haploinsufficiency Scores

• pHI: 0.618
• hipred: N
• hipred_score: 0.281
• ghis: 0.609

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.747

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rpl28

Zebrafish Information Network

• Gene name: rpl28
• Affected structure: anatomical system
• Phenotype tag: abnormal
• Phenotype quality: quality

Gene ontology

• Biological process: nuclear-transcribed mRNA catabolic process, nonsense-mediated decay;translation;translational initiation;SRP-dependent cotranslational protein targeting to membrane
• Cellular component: cytosol;membrane;cytosolic large ribosomal subunit;dendrite;cytoplasmic ribonucleoprotein granule;cell body;extracellular exosome
• Molecular function: RNA binding;structural constituent of ribosome;protein binding