RPL10L

ribosomal protein L10 like, the group of L ribosomal proteins

Basic information

Region (hg38): 14:46651010-46651781

Links

ENSG00000165496 ∙ NCBI:140801 ∙ OMIM:619655 ∙ HGNC:17976 ∙ Uniprot:Q96L21 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• spermatogenic failure 63 (Limited), mode of inheritance: Unknown

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Spermatogenic failure 63	AR	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	Genitourinary	32111475

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the RPL10L gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RPL10L 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		1	30			31
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	1	30	0	0

Variants in RPL10L

This is a list of pathogenic ClinVar variants found in the RPL10L region.

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

Position	Type	Phenotype	Significance	ClinVar
14-46651108-C-T		not specified	Uncertain significance (Sep 01, 2021)
14-46651109-G-A		not specified	Uncertain significance (Aug 16, 2022)
14-46651160-C-T		not specified	Uncertain significance (Nov 14, 2023)
14-46651169-G-A		not specified	Uncertain significance (Oct 25, 2022)
14-46651184-C-T		not specified	Uncertain significance (Dec 16, 2024)
14-46651186-A-G		not specified	Uncertain significance (Dec 10, 2024)
14-46651235-A-T		not specified	Uncertain significance (Jul 05, 2022)
14-46651236-G-C		Intellectual developmental disorder with dysmorphic facies and ptosis	Uncertain significance (May 19, 2020)
14-46651240-T-C		not specified	Uncertain significance (Sep 04, 2024)
14-46651247-T-C		not specified	Uncertain significance (Jul 26, 2021)
14-46651255-C-A		not specified	Uncertain significance (Apr 05, 2023)
14-46651286-C-A		not specified	Uncertain significance (Mar 28, 2023)
14-46651291-A-G		not specified	Uncertain significance (Mar 15, 2024)
14-46651338-T-C		EBV-positive nodal T- and NK-cell lymphoma	Likely benign (-)
14-46651351-A-G		not specified	Uncertain significance (Aug 30, 2021)
14-46651354-C-T		not specified	Uncertain significance (Jul 20, 2022)
14-46651423-C-A		not specified	Uncertain significance (Oct 12, 2022)
14-46651435-T-C		not specified	Uncertain significance (Mar 01, 2023)
14-46651444-C-T		EBV-positive nodal T- and NK-cell lymphoma	Likely benign (-)
14-46651445-G-A		not specified	Uncertain significance (Mar 04, 2024)
14-46651468-C-T		not specified	Uncertain significance (Sep 26, 2024)
14-46651469-G-A		not specified	Uncertain significance (Jun 22, 2021)
14-46651474-C-T		not specified	Uncertain significance (Feb 07, 2025)
14-46651480-T-G		Spermatogenesis maturation arrest • Spermatogenic failure 63	Likely pathogenic (Feb 25, 2020)
14-46651516-T-C		not specified	Uncertain significance (Sep 04, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RPL10L	protein_coding	protein_coding	ENST00000298283	1	807

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00517	0.719	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.245	146	138	1.06	0.00000932	1412
Missense in Polyphen		20	21.06	0.94967		298
Synonymous	-2.50	70	47.9	1.46	0.00000275	425
Loss of Function	0.754	4	5.99	0.668	5.10e-7	57

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: May play a role in compensating for the inactivated X- linked gene during spermatogenesis. {ECO:0000269|PubMed:12490704}.
• Pathway: Ribosome - Homo sapiens (human);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: 0.123

Intolerance Scores

• rvis_EVS: 0.17
• rvis_percentile_EVS: 65.76

Haploinsufficiency Scores

• pHI: 0.979
• hipred: N
• hipred_score: 0.471
• ghis: 0.424

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.127

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rpl10l

Gene ontology

• Biological process: ribosomal large subunit assembly;translation;spermatogenesis
• Cellular component: nucleus;endoplasmic reticulum;cytosol;polysome;membrane;cytosolic large ribosomal subunit
• Molecular function: structural constituent of ribosome