RSL1D1

ribosomal L1 domain containing 1, the group of SSU processome

Basic information

Region (hg38): 16:11833849-11851580

Links

ENSG00000171490 ∙ NCBI:26156 ∙ OMIM:615874 ∙ HGNC:24534 ∙ Uniprot:O76021 ∙ 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 RSL1D1 gene.

• Inborn genetic diseases (15 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RSL1D1 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			14	1		15
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	14	1	0

Variants in RSL1D1

This is a list of pathogenic ClinVar variants found in the RSL1D1 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-11837826-T-G		not specified	Uncertain significance (Jun 17, 2022)
16-11837851-A-G		not specified	Likely benign (Jan 24, 2024)
16-11837965-G-C		not specified	Likely benign (Dec 11, 2023)
16-11838052-C-T		not specified	Uncertain significance (Dec 13, 2022)
16-11838065-G-C		not specified	Uncertain significance (Sep 26, 2023)
16-11838073-C-A		not specified	Uncertain significance (Mar 31, 2023)
16-11838083-G-A		not specified	Uncertain significance (Dec 22, 2023)
16-11839706-C-G		not specified	Uncertain significance (Jul 13, 2021)
16-11839721-T-G		not specified	Uncertain significance (Jan 23, 2024)
16-11839799-G-A		not specified	Uncertain significance (Dec 05, 2022)
16-11841816-C-A		not specified	Uncertain significance (Nov 08, 2022)
16-11841819-T-C		not specified	Uncertain significance (Dec 01, 2022)
16-11846544-T-A		not specified	Uncertain significance (Oct 06, 2021)
16-11846598-G-A		not specified	Uncertain significance (Feb 17, 2022)
16-11846732-G-A		not specified	Uncertain significance (Nov 14, 2023)
16-11847661-T-A			Likely benign (May 01, 2023)
16-11847676-C-T		not specified	Likely benign (Dec 15, 2022)
16-11847783-G-A		not specified	Uncertain significance (Aug 19, 2023)
16-11847804-G-A		not specified	Uncertain significance (Oct 20, 2021)
16-11847805-T-C		not specified	Uncertain significance (Apr 07, 2022)
16-11850342-T-C		not specified	Likely benign (Feb 05, 2024)
16-11850383-G-C		not specified	Uncertain significance (Feb 02, 2022)
16-11851463-G-A		not specified	Uncertain significance (Sep 13, 2022)
16-11851490-G-A		not specified	Uncertain significance (Feb 01, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RSL1D1	protein_coding	protein_coding	ENST00000571133	9	16387

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.17e-7	0.864	125720	0	19	125739	0.0000756

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.61	325	253	1.29	0.0000130	3181
Missense in Polyphen		67	62.269	1.076		831
Synonymous	-3.16	135	95.6	1.41	0.00000518	942
Loss of Function	1.54	13	20.6	0.632	0.00000103	282

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000275	0.000275
Ashkenazi Jewish	0.000298	0.000298
East Asian	0.00	0.00
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000634	0.0000615
Middle Eastern	0.00	0.00
South Asian	0.0000657	0.0000653
Other	0.000166	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Regulates cellular senescence through inhibition of PTEN translation. Acts as a pro-apoptotic regulator in response to DNA damage. {ECO:0000269|PubMed:18678645, ECO:0000269|PubMed:22419112}.
• Pathway: Senescence and Autophagy in Cancer (Consensus)

Recessive Scores

• pRec: 0.0973

Intolerance Scores

• loftool: 0.485
• rvis_EVS: -0.11
• rvis_percentile_EVS: 45.49

Haploinsufficiency Scores

• pHI: 0.818
• hipred: Y
• hipred_score: 0.539
• ghis: 0.560

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.841

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rsl1d1

Gene ontology

• Biological process: maturation of LSU-rRNA;osteoblast differentiation;regulation of protein localization;regulation of apoptotic process;regulation of cellular senescence
• Cellular component: nucleolus;membrane;90S preribosome
• Molecular function: RNA binding;mRNA 3'-UTR binding;cadherin binding;mRNA 5'-UTR binding