LTO1

protein-coding

LTO1 maturation factor of ABCE1

Gene summary

Involved in protein maturation; ribosomal large subunit biogenesis; and translational initiation. Predicted to be located in nucleus. [provided by Alliance of Genome Resources, Jun 2026]

Previous symbols:

ORAOV1

MANE transcript

NM_153451.3

Inheritance

—

ClinVar variants

U:21B:1

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.66

Max pathogenic AF

—

Genomic locus

chr11:69,653,076-69,675,416

External References & Databases

Ensembl (ENSG00000149716)

Transcript & Mutation Effects

hg38 • Region Span ~22.3 kb

Loading mutation effect viewer...

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 LTO1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 23

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_153451.3. 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						0
missense			21 clinvar	1 clinvar		22
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	21	1	0	22

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 24 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_153451.3	RefSeq	NP_703152.1	5	MANE Select
ENST00000279147.9	Ensembl	ENSP00000279147.5	5	MANE Select
ENST00000441922.6	Ensembl	ENSP00000409643.2	3	Standard
ENST00000535542.5	Ensembl	ENSP00000443669.1	2	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

telomere maintenance
translational initiation
ribosomal large subunit biogenesis
protein maturation by [4Fe-4S] cluster transfer

Molecular Function

molecular_function
protein binding

Cellular Component

cellular_component
nucleus

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000279147
Coding exons: 5
Length: 22341
Individuals with no LoFs: 125736
Homozygous LoFs: 0
Heterozygous LoFs: 12
Defined: 125748
p: 0.0000477

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.411	84	74.1	1.13	0.00000379	910
Missense (PolyPhen)		13	16.627	0.78184		201
Synonymous	0.760	23	28.1	0.818	0.00000166	228
Loss of Function	0.859	5	7.55	0.663	3.17e-7	98

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00031	0.00031	rare
Latino/Admixed American	0.000029	0.000029	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00011	0.000054	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000035	0.000035	rare
South Asian	0	0.0	absent
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: The complex LTO1:YAE1 functions as a target specific adapter that probably recruits apo-ABCE1 to the cytosolic iron- sulfur protein assembly (CIA) complex machinery (PubMed:26182403). May be required for biogenesis of the large ribosomal subunit and initiation of translation (PubMed:23318452). May play a role in the regulation of proline metabolism and ROS production (PubMed:24930674). {ECO:0000269|PubMed:23318452, ECO:0000269|PubMed:24930674, ECO:0000269|PubMed:26182403}.;

Recessive Scores

pRec: 0.127

Intolerance Scores

RVIS EVS: 0.08
RVIS percentile EVS: 59.76

Essentials

Essential (gene trap): E