OSGEPL1

protein-coding

O-sialoglycoprotein endopeptidase like 1

Gene summary

Enables tRNA N(6)-L-threonylcarbamoyladenine synthase activity. Involved in tRNA threonylcarbamoyladenosine modification. Is active in mitochondrion. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_022353.3

Inheritance

—

ClinVar variants

U:49B:3

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.57

Max pathogenic AF

—

Genomic locus

chr2:189,746,660-189,763,227

External References & Databases

Ensembl (ENSG00000128694)

Transcript & Mutation Effects

hg38 • Region Span ~16.6 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 OSGEPL1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 46

not providedTotal: 4

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_022353.3. 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					1 clinvar	1
missense			49 clinvar		1 clinvar	50
nonsense						0
start loss						0
frameshift				1 clinvar		1
splice donor/acceptor (+/-2bp)						0
Total	0	0	49	1	2	52

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 52 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_022353.3	RefSeq	NP_071748.2	7	MANE Select
ENST00000264151.10	Ensembl	ENSP00000264151.5	7	MANE Select
NM_001354347.2	RefSeq	NP_001341276.2	7	Standard
NM_001376077.1	RefSeq	NP_001363006.1	7	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

tRNA threonylcarbamoyladenosine modification
proteolysis

Molecular Function

metalloendopeptidase activity
metal ion binding
N(6)-L-threonylcarbamoyladenine synthase activity

Cellular Component

EKC/KEOPS complex
mitochondrion

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000264151
Coding exons: 7
Length: 16568
Individuals with no LoFs: 123873
Homozygous LoFs: 0
Heterozygous LoFs: 759
Defined: 124632
p: 0.00305

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.792	176	208	0.845	0.00000981	2676
Missense (PolyPhen)		63	81.222	0.77565		1043
Synonymous	1.21	55	67.6	0.813	0.00000306	815
Loss of Function	1.58	9	15.8	0.570	7.46e-7	232

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00052	0.00052	rare
Latino/Admixed American	0.0012	0.0011	notable
Ashkenazi Jewish	0.0027	0.0027	notable
East Asian	0.00011	0.00011	rare
Finnish	0.0033	0.0033	notable
European (Non-Finnish)	0.0050	0.0050	notable
South Asian	0.00076	0.00075	rare
Other	0.0038	0.0038	notable

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Required for the formation of a threonylcarbamoyl group on adenosine at position 37 (t(6)A37) in mitochondrial tRNAs that read codons beginning with adenine. Probably involved in the transfer of the threonylcarbamoyl moiety of threonylcarbamoyl-AMP (TC-AMP) to the N6 group of A37. Involved in mitochondrial genome maintenance. {ECO:0000255|HAMAP-Rule:MF_03179}.;

Recessive Scores

pRec: 0.103

Intolerance Scores

LoFtool: 0.743
RVIS EVS: -0.03
RVIS percentile EVS: 51.66

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.399

Gene Damage Prediction

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