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RPL10

ribosomal protein L10, the group of Small nucleolar RNA protein coding host genes|L ribosomal proteins

Basic information

Region (hg38): X:154389954-154409168

Links

ENSG00000147403NCBI:6134OMIM:312173HGNC:10298Uniprot:P27635AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

  • intellectual disability, X-linked, syndromic, 35 (Definitive), mode of inheritance: XLR
  • X-linked microcephaly-growth retardation-prognathism-cryptorchidism syndrome (Supportive), mode of inheritance: XL
  • X-linked intellectual disability-cerebellar hypoplasia-spondylo-epiphyseal dysplasia syndrome (Supportive), mode of inheritance: XL
  • autism, susceptibility to, X-linked 5 (Limited), mode of inheritance: XL
  • intellectual disability, X-linked, syndromic, 35 (Moderate), mode of inheritance: XL
  • intellectual disability, X-linked, syndromic, 35 (Definitive), mode of inheritance: XL
  • autism, susceptibility to, X-linked 5 (Limited), mode of inheritance: Unknown
  • intellectual disability, X-linked, syndromic, 35 (Strong), mode of inheritance: XL
  • X-linked syndromic intellectual disability (Moderate), mode of inheritance: XL

Clinical Genomic Database

Source: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Intellectual developmental disorder, X-linked, syndromic, 35XLGeneralGenetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testingCraniofacial; Genitourinary; Musculoskeletal; Neurologic25316788; 25846674; 26290468

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the RPL10 gene.

  • not provided (25 variants)
  • Inborn genetic diseases (12 variants)
  • Intellectual disability, X-linked, syndromic, 35 (8 variants)
  • not specified (4 variants)
  • RPL10-related condition (1 variants)
  • Autism, susceptibility to, X-linked 5 (1 variants)
  • See cases (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RPL10 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
4
clinvar
4
missense
1
clinvar
3
clinvar
13
clinvar
2
clinvar
4
clinvar
23
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
4
2
6
non coding
6
clinvar
4
clinvar
2
clinvar
12
Total 1 3 19 10 6

Variants in RPL10

This is a list of pathogenic ClinVar variants found in the RPL10 region.

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

Position Type Phenotype Significance ClinVar
X-154398396-T-G Uncertain significance (Jun 23, 2022)1806502
X-154398397-G-A Intellectual disability, X-linked, syndromic, 35 Benign (Nov 07, 2021)1327969
X-154398516-C-T Uncertain significance (May 01, 2018)807865
X-154398527-G-A Likely pathogenic (Nov 15, 2015)431945
X-154398551-T-A not specified Benign (Feb 12, 2015)130161
X-154399325-C-T not specified Uncertain significance (May 04, 2022)1685077
X-154399328-T-C Likely benign (Jul 12, 2018)760581
X-154399330-C-G Uncertain significance (Dec 01, 2023)3024976
X-154399356-C-A Inborn genetic diseases Likely benign (Jun 30, 2023)2609304
X-154399525-G-A Uncertain significance (Feb 14, 2020)1314146
X-154399596-T-TA Likely benign (Jun 01, 2022)1695325
X-154399601-C-T Uncertain significance (Oct 01, 2021)1176612
X-154399793-C-T See cases Uncertain significance (Nov 29, 2021)1690503
X-154399798-C-T Intellectual disability, X-linked, syndromic, 35 Uncertain significance (Mar 04, 2019)1028473
X-154399803-C-T Intellectual disability, X-linked, syndromic, 35 Pathogenic (Apr 01, 2024)430614
X-154399826-G-A Intellectual disability, X-linked, syndromic, 35;Autism, susceptibility to, X-linked 5 Uncertain significance (-)3024241
X-154399830-A-C Intellectual disability, X-linked, syndromic, 35 Uncertain significance (Apr 29, 2022)1679194
X-154399836-A-T Inborn genetic diseases Uncertain significance (Jul 06, 2021)2234615
X-154399844-A-G Intellectual disability, X-linked, syndromic, 35 Pathogenic (Aug 30, 2019)430612
X-154399848-G-C Intellectual disability, X-linked, syndromic, 35 Uncertain significance (Aug 09, 2019)931462
X-154399863-G-A Uncertain significance (Feb 01, 2019)807866
X-154399864-C-T Inborn genetic diseases Likely benign (Dec 27, 2017)1792661
X-154399876-G-A Inborn genetic diseases Likely benign (Apr 11, 2017)588816
X-154399903-C-T Inborn genetic diseases Conflicting classifications of pathogenicity (Apr 04, 2017)167612
X-154399947-C-G RPL10-related condition Uncertain significance (Jan 07, 2023)2629407

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
RPL10protein_codingprotein_codingENST00000424325 619190
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.9090.090200000.00
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense2.612089.60.2230.000007221401
Missense in Polyphen113.3610.074846295
Synonymous-1.083931.31.250.00000219411
Loss of Function2.5807.730.006.13e-7126

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.000.00
Ashkenazi Jewish0.000.00
East Asian0.000.00
Finnish0.000.00
European (Non-Finnish)0.000.00
Middle Eastern0.000.00
South Asian0.000.00
Other0.000.00

dbNSFP

Source: dbNSFP

Function
FUNCTION: Component of the large ribosomal subunit (PubMed:26290468). Plays a role in the formation of actively translating ribosomes (PubMed:26290468). May play a role in the embryonic brain development (PubMed:25316788). {ECO:0000269|PubMed:25316788, ECO:0000269|PubMed:26290468, ECO:0000305|PubMed:12962325}.;
Disease
DISEASE: Autism, X-linked 5 (AUTSX5) [MIM:300847]: A complex multifactorial, pervasive developmental disorder characterized by impairments in reciprocal social interaction and communication, restricted and stereotyped patterns of interests and activities, and the presence of developmental abnormalities by 3 years of age. Most individuals with autism also manifest moderate mental retardation. {ECO:0000269|PubMed:16940977, ECO:0000269|PubMed:21567917, ECO:0000269|PubMed:25316788}. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry. RPL10 is involved in autism only in rare cases. Two hypomorphic variants affecting the translation process have been found in families with autism spectrum disorders, suggesting that aberrant translation may play a role in disease mechanisms.; DISEASE: Mental retardation, X-linked, syndromic, 35 (MRXS35) [MIM:300998]: A mental retardation syndrome characterized by intellectual deficit, delayed psychomotor development, poor speech, and dysmorphic features. Mental retardation is defined by significantly below average general intellectual functioning associated with impairments in adaptive behavior and manifested during the developmental period. {ECO:0000269|PubMed:25316788, ECO:0000269|PubMed:25846674, ECO:0000269|PubMed:26290468}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
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
0.381

Intolerance Scores

loftool
rvis_EVS
0.04
rvis_percentile_EVS
56.25

Haploinsufficiency Scores

pHI
0.281
hipred
Y
hipred_score
0.743
ghis
0.505

Essentials

essential_gene_CRISPR
E
essential_gene_CRISPR2
E
essential_gene_gene_trap
gene_indispensability_pred
N
gene_indispensability_score
0.312

Gene Damage Prediction

AllRecessiveDominant
MendelianLowLowLow
Primary ImmunodeficiencyMediumLowMedium
CancerLowLowLow

Mouse Genome Informatics

Gene name
Rpl10
Phenotype

Zebrafish Information Network

Gene name
rpl10
Affected structure
head
Phenotype tag
abnormal
Phenotype quality
decreased size

Gene ontology

Biological process
ribosomal large subunit assembly;negative regulation of transcription by RNA polymerase II;nuclear-transcribed mRNA catabolic process, nonsense-mediated decay;translation;translational initiation;regulation of translation;SRP-dependent cotranslational protein targeting to membrane;negative regulation of apoptotic process;embryonic brain development
Cellular component
nucleus;endoplasmic reticulum;smooth endoplasmic reticulum;cytosol;membrane;cytosolic large ribosomal subunit;protein-containing complex
Molecular function
RNA binding;structural constituent of ribosome;protein binding;translation regulator activity