OSGEPL1

O-sialoglycoprotein endopeptidase like 1

Basic information

Region (hg38): 2:189746660-189763227

Links

ENSG00000128694 ∙ NCBI:64172 ∙ OMIM:619634 ∙ HGNC:23075 ∙ Uniprot:Q9H4B0 ∙ 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 OSGEPL1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the OSGEPL1 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	18
nonsense						0
start loss						0
frameshift				1		1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	17	1	2

Variants in OSGEPL1

This is a list of pathogenic ClinVar variants found in the OSGEPL1 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-189752685-T-TA			Likely benign (Jul 01, 2024)
2-189752708-G-C		not specified	Uncertain significance (Nov 14, 2023)
2-189752714-C-G		not specified	Uncertain significance (Jul 27, 2021)
2-189752940-T-C		not specified	Uncertain significance (Oct 17, 2023)
2-189752942-C-A		not specified	Uncertain significance (May 16, 2024)
2-189752961-C-T		not specified	Uncertain significance (Feb 16, 2023)
2-189752973-A-C		not specified	Uncertain significance (Nov 18, 2022)
2-189753971-C-T		not specified	Uncertain significance (Jul 20, 2021)
2-189754002-T-C		not specified	Uncertain significance (Jul 14, 2023)
2-189754014-C-T		not specified	Uncertain significance (Feb 28, 2023)
2-189754274-A-G			Benign (Aug 20, 2018)
2-189754302-G-T		not specified	Uncertain significance (Mar 16, 2022)
2-189755207-G-C			Uncertain significance (-)
2-189755261-T-G		not specified	Uncertain significance (Feb 23, 2023)
2-189755286-A-T		not specified	Uncertain significance (Feb 03, 2022)
2-189755325-G-A		not specified	Uncertain significance (Nov 09, 2021)
2-189755405-A-G		not specified	Uncertain significance (Nov 21, 2023)
2-189755406-C-T		not specified	Uncertain significance (Apr 18, 2023)
2-189755471-A-T		not specified	Uncertain significance (Apr 25, 2022)
2-189761517-T-A		not specified	Uncertain significance (Aug 23, 2021)
2-189761529-T-C		not specified	Uncertain significance (Jun 10, 2024)
2-189761562-T-G			Benign (Aug 20, 2018)
2-189761603-T-A		not specified	Uncertain significance (Jul 26, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
OSGEPL1	protein_coding	protein_coding	ENST00000264151	7	16568

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000673	0.915	123873	0	759	124632	0.00305

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.792	176	208	0.845	0.00000981	2676
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00170	0.00170
Ashkenazi Jewish	0.00268	0.00269
East Asian	0.000115	0.000111
Finnish	0.00326	0.00325
European (Non-Finnish)	0.00503	0.00503
Middle Eastern	0.000115	0.000111
South Asian	0.000758	0.000752
Other	0.00381	0.00381

dbNSFP

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

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.167
• ghis: 0.571

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.399

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Osgepl1

Gene ontology

• Biological process: tRNA threonylcarbamoyladenosine modification;proteolysis
• Cellular component: EKC/KEOPS complex;mitochondrion
• Molecular function: metalloendopeptidase activity;metal ion binding;N(6)-L-threonylcarbamoyladenine synthase activity