RCL1

protein-coding

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

Gene summary

Predicted to enable RNA endonuclease activity. Involved in ribosomal small subunit biogenesis. Part of small-subunit processome. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_005772.5

Inheritance

—

ClinVar variants

P:1U:65B:3

Top phenotype

Psychotic disorder

gnomAD constraint

pLI —, LoF o/e 0.29

Max pathogenic AF

—

Genomic locus

chr9:4,792,944-4,885,917

External References & Databases

Ensembl (ENSG00000120158)

Transcript & Mutation Effects

hg38 • Region Span ~93.0 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to RCL1 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 64

not providedTotal: 2

Psychotic disorderTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_005772.5. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous				1 clinvar	1 clinvar	2
missense			64 clinvar	1 clinvar		65
nonsense	1 clinvar					1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	1	0	65	2	1	69

Highest pathogenic variant AF is 0.0000018586785

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 25 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_005772.5	RefSeq	NP_005763.3	9	MANE Select
ENST00000381750.9	Ensembl	ENSP00000371169.4	9	MANE Select
NM_001286699.2	RefSeq	NP_001273628.1	5	Standard
NM_001286700.2	RefSeq	NP_001273629.1	5	Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / Model	Organism	Observed Phenotype
rcl1	Danio rerio	Structure: head Quality: decreased size abnormal

Gene / Model

Organism

Observed Phenotype

rcl1

Danio rerio

Structure: head

Quality: decreased size

abnormal

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

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

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

Molecular Function

endoribonuclease activity

Cellular Component

nucleoplasm
nucleolus

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000381750
Coding exons: 9
Length: 93049
Individuals with no LoFs: 125740
Homozygous LoFs: 0
Heterozygous LoFs: 8
Defined: 125748
p: 0.0000318

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-1.05	258	215	1.20	0.0000116	2389
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000030	0.000029	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.000053	0.000053	rare
South Asian	0.000033	0.000033	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

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}.;

Recessive Scores

pRec: 0.115

Intolerance Scores

LoFtool: 0.0852
RVIS EVS: 0.4
RVIS percentile EVS: 76.31

Essentials

Essential (CRISPR): E
Essential (CRISPR2): E
Essential (gene trap): E
Indispensability pred.: N
Indispensability score: 0.435

Gene Damage Prediction

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