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
Phenotypes
GenCC
Source:
- 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
- X-linked syndromic intellectual disability (Moderate), mode of inheritance: XL
Clinical Genomic Database
Source:
| Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
|---|---|---|---|---|---|
| Intellectual developmental disorder, X-linked, syndromic, 35 | XL | General | Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing | Craniofacial; Genitourinary; Musculoskeletal; Neurologic | 25316788; 25846674; 26290468 |
ClinVar
This is a list of variants' phenotypes submitted to
- not provided (22 variants)
- Inborn genetic diseases (12 variants)
- Intellectual disability, X-linked, syndromic, 35 (11 variants)
- not specified (4 variants)
- Autism, susceptibility to, X-linked 5 (2 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.
| Variant type | Pathogenic | Likely pathogenic | VUS | Likely benign | Benign | Sum |
|---|---|---|---|---|---|---|
| synonymous | 3 | 3 | ||||
| missense | 3 | 3 | 14 | 1 | 4 | 25 |
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice variant | 4 | 2 | 1 | 7 | ||
| non coding | 5 | 2 | 3 | 10 | ||
| Total | 3 | 3 | 23 | 8 | 8 |
Variants in RPL10
This is a list of pathogenic ClinVar variants found in the RPL10 region.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| X-154398396-T-G | Uncertain significance (Jun 23, 2022) | |||
| X-154398397-G-A | Intellectual disability, X-linked, syndromic, 35 | Benign (Nov 07, 2021) | ||
| X-154398516-C-T | Uncertain significance (May 01, 2018) | |||
| X-154398527-G-A | Likely pathogenic (Nov 15, 2015) | |||
| X-154398551-T-A | not specified | Benign (Feb 12, 2015) | ||
| X-154399325-C-T | not specified | Uncertain significance (May 04, 2022) | ||
| X-154399328-T-C | Likely benign (Jul 12, 2018) | |||
| X-154399356-C-A | Inborn genetic diseases | Likely benign (Jun 30, 2023) | ||
| X-154399525-G-A | Uncertain significance (Feb 14, 2020) | |||
| X-154399596-T-TA | Likely benign (Jun 01, 2022) | |||
| X-154399601-C-T | Uncertain significance (Oct 01, 2021) | |||
| X-154399793-C-T | See cases | Uncertain significance (Nov 29, 2021) | ||
| X-154399798-C-T | Intellectual disability, X-linked, syndromic, 35 | Uncertain significance (Mar 04, 2019) | ||
| X-154399803-C-T | Intellectual disability, X-linked, syndromic, 35 | Pathogenic (Aug 19, 2021) | ||
| X-154399830-A-C | Intellectual disability, X-linked, syndromic, 35 | Uncertain significance (Apr 29, 2022) | ||
| X-154399836-A-T | Inborn genetic diseases | Uncertain significance (Jul 06, 2021) | ||
| X-154399844-A-G | Intellectual disability, X-linked, syndromic, 35 | Pathogenic (Aug 30, 2019) | ||
| X-154399848-G-C | Intellectual disability, X-linked, syndromic, 35 | Uncertain significance (Aug 09, 2019) | ||
| X-154399863-G-A | Uncertain significance (Feb 01, 2019) | |||
| X-154399864-C-T | Inborn genetic diseases | Likely benign (Dec 27, 2017) | ||
| X-154399876-G-A | Inborn genetic diseases | Likely benign (Apr 11, 2017) | ||
| X-154399903-C-T | Inborn genetic diseases | Conflicting interpretations of pathogenicity (Apr 04, 2017) | ||
| X-154400457-A-G | Likely benign (Dec 31, 2019) | |||
| X-154400481-G-A | Intellectual disability, X-linked, syndromic, 35 | Uncertain significance (Oct 05, 2018) | ||
| X-154400601-A-C | Uncertain significance (Jan 18, 2021) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| RPL10 | protein_coding | protein_coding | ENST00000424325 | 6 | 19190 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.909 | 0.0902 | 0 | 0 | 0 | 0 | 0.00 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 2.61 | 20 | 89.6 | 0.223 | 0.00000722 | 1401 |
| Missense in Polyphen | 1 | 13.361 | 0.074846 | 295 | ||
| Synonymous | -1.08 | 39 | 31.3 | 1.25 | 0.00000219 | 411 |
| Loss of Function | 2.58 | 0 | 7.73 | 0.00 | 6.13e-7 | 126 |
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:
- 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
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Low | Low | Low |
| Primary Immunodeficiency | Medium | Low | Medium |
| Cancer | Low | Low | Low |
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