RCL1

RNA terminal phosphate cyclase like 1, the group of MicroRNA protein coding host genes|SSU processome

Basic information

Region (hg38): 9:4792943-4885917

Links

ENSG00000120158 ∙ NCBI:10171 ∙ OMIM:611405 ∙ HGNC:17687 ∙ Uniprot:Q9Y2P8 ∙ 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 RCL1 gene.

• Inborn genetic diseases (18 variants)
• not provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RCL1 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					1	1
missense			17	1	1	19
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	17	1	2

Variants in RCL1

This is a list of pathogenic ClinVar variants found in the RCL1 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-4793179-G-C		not specified	Uncertain significance (Jul 05, 2023)
9-4793188-C-G		not specified	Uncertain significance (Dec 19, 2023)
9-4823579-C-A		not specified	Uncertain significance (Oct 12, 2022)
9-4823587-C-T		not specified	Uncertain significance (Jun 24, 2022)
9-4823599-G-A		not specified	Uncertain significance (Apr 20, 2023)
9-4826906-A-C		not specified	Uncertain significance (Jan 29, 2024)
9-4826920-G-A		not specified	Uncertain significance (Feb 26, 2024)
9-4826926-C-T		not specified	Uncertain significance (Dec 09, 2023)
9-4826927-G-A		not specified	Uncertain significance (Feb 03, 2022)
9-4827014-A-G		not specified	Uncertain significance (Jan 07, 2022)
9-4827019-C-T		Psychotic disorder	Pathogenic (Nov 05, 2020)
9-4833178-C-T		not specified	Uncertain significance (Oct 25, 2023)
9-4833202-A-C		not specified	Uncertain significance (Sep 17, 2021)
9-4834150-C-T		not specified	Uncertain significance (Jan 03, 2024)
9-4841222-C-T			Benign (Mar 05, 2018)
9-4841245-G-A		not specified	Uncertain significance (Sep 01, 2021)
9-4841290-A-C		not specified	Uncertain significance (Mar 24, 2023)
9-4841337-G-C		not specified	Uncertain significance (Aug 12, 2021)
9-4844566-G-A		not specified	Likely benign (Apr 26, 2023)
9-4844656-G-A		not specified	Uncertain significance (May 22, 2023)
9-4849463-C-T		not specified	Uncertain significance (Feb 13, 2024)
9-4849515-T-C			Benign (Apr 23, 2018)
9-4849520-A-G		not specified	Uncertain significance (Nov 05, 2021)
9-4849526-T-C		not specified	Uncertain significance (May 15, 2023)
9-4860138-C-T		not specified	Uncertain significance (Sep 29, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RCL1	protein_coding	protein_coding	ENST00000381750	9	93049

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0594	0.940	125740	0	8	125748	0.0000318

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.05	258	215	1.20	0.0000116	2389
Missense in Polyphen		79	76.659	1.0305		857
Synonymous	-2.08	105	81.2	1.29	0.00000423	774
Loss of Function	2.98	6	20.6	0.291	0.00000132	219

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000299	0.0000299
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000532	0.0000527
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Does not have cyclase activity. Plays a role in 40S- ribosomal-subunit biogenesis in the early pre-rRNA processing steps at sites A0, A1 and A2 that are required for proper maturation of the 18S RNA (By similarity). {ECO:0000250}.
• Pathway: Ribosome biogenesis in eukaryotes - Homo sapiens (human);rRNA processing;Metabolism of RNA;rRNA modification in the nucleus and cytosol;rRNA processing in the nucleus and cytosol (Consensus)

Recessive Scores

• pRec: 0.115

Intolerance Scores

• loftool: 0.0852
• rvis_EVS: 0.4
• rvis_percentile_EVS: 76.31

Haploinsufficiency Scores

• pHI: 0.518
• hipred: Y
• hipred_score: 0.631
• ghis: 0.402

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: N
• gene_indispensability_score: 0.435

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rcl1

Zebrafish Information Network

• Gene name: rcl1
• Affected structure: head
• Phenotype tag: abnormal
• Phenotype quality: decreased size

Gene ontology

• Biological process: endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA);endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA);rRNA processing;biological_process
• Cellular component: nucleoplasm;nucleolus
• Molecular function: endoribonuclease activity