RPL10A

ribosomal protein L10a, the group of L ribosomal proteins|MicroRNA protein coding host genes

Basic information

Region (hg38): 6:35468400-35470785

Previous symbols: [ "NEDD6" ]

Links

ENSG00000198755 ∙ NCBI:4736 ∙ OMIM:615660 ∙ HGNC:10299 ∙ Uniprot:P62906 ∙ 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 RPL10A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RPL10A 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						0
Total	0	0	4	0	0

Variants in RPL10A

This is a list of pathogenic ClinVar variants found in the RPL10A region.

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

Position	Type	Phenotype	Significance	ClinVar
6-35468809-T-C		not specified	Uncertain significance (Sep 13, 2023)
6-35468867-G-A		not specified	Uncertain significance (Mar 20, 2023)
6-35469410-C-G		not specified	Uncertain significance (Feb 06, 2023)
6-35470700-C-T		not specified	Uncertain significance (Jan 23, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RPL10A	protein_coding	protein_coding	ENST00000322203	6	2378

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.854	0.146	125737	0	9	125746	0.0000358

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.06	58	122	0.475	0.00000598	1420
Missense in Polyphen		6	19.333	0.31035		308
Synonymous	-0.625	57	51.3	1.11	0.00000268	407
Loss of Function	2.75	1	10.7	0.0936	5.20e-7	135

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000290	0.0000290
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000442	0.0000439
Middle Eastern	0.000109	0.000109
South Asian	0.00	0.00
Other	0.000164	0.000163

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)

Intolerance Scores

• rvis_EVS: -0.19
• rvis_percentile_EVS: 39.68

Haploinsufficiency Scores

• pHI: 0.891
• hipred: Y
• hipred_score: 0.754
• ghis: 0.654

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.969

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rpl10a

Gene ontology

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