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

ENSG00000147403 ∙ NCBI:6134 ∙ OMIM:312173 ∙ HGNC:10298 ∙ Uniprot:P27635 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

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

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 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		4
missense	1	3	13	2	4	23
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region			4	2		6
non coding			6	4	2	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)
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-154399330-C-G			Uncertain significance (Dec 01, 2023)
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 (Apr 01, 2024)
X-154399826-G-A		Intellectual disability, X-linked, syndromic, 35;Autism, susceptibility to, X-linked 5	Uncertain significance (-)
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 classifications of pathogenicity (Apr 04, 2017)
X-154399947-C-G		RPL10-related disorder	Uncertain significance (Jan 07, 2023)

GnomAD

Source: gnomAD

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: 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

• 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
• 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

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