THOP1

thimet oligopeptidase 1, the group of M3 metallopeptidase family

Basic information

Region (hg38): 19:2785503-2815807

Links

ENSG00000172009 ∙ NCBI:7064 ∙ OMIM:601117 ∙ HGNC:11793 ∙ Uniprot:P52888 ∙ 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 THOP1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the THOP1 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						0
missense			52	2		54
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	52	2	0

Variants in THOP1

This is a list of pathogenic ClinVar variants found in the THOP1 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-2790444-G-A		not specified	Uncertain significance (Jul 12, 2022)
19-2790478-G-A		not specified	Uncertain significance (Feb 27, 2023)
19-2790612-G-A		not specified	Uncertain significance (Oct 25, 2022)
19-2790624-A-G		not specified	Uncertain significance (Feb 07, 2023)
19-2790628-A-G		not specified	Uncertain significance (Mar 31, 2023)
19-2794859-G-A		not specified	Uncertain significance (Aug 08, 2022)
19-2794878-G-C		not specified	Uncertain significance (Oct 06, 2022)
19-2796099-T-C		not specified	Uncertain significance (Jul 19, 2022)
19-2796118-C-T		not specified	Uncertain significance (Sep 01, 2021)
19-2796150-C-T		not specified	Uncertain significance (Jun 24, 2022)
19-2799701-A-T		not specified	Uncertain significance (Jun 01, 2022)
19-2799777-C-T		not specified	Uncertain significance (Feb 17, 2022)
19-2799783-A-G		not specified	Uncertain significance (May 07, 2024)
19-2805166-G-A		not specified	Uncertain significance (Sep 22, 2023)
19-2805171-A-G		not specified	Uncertain significance (Dec 03, 2021)
19-2807029-G-A		not specified	Uncertain significance (May 11, 2022)
19-2807037-G-A		not specified	Uncertain significance (Nov 18, 2022)
19-2807041-C-T		not specified	Uncertain significance (May 25, 2022)
19-2807451-C-T		not specified	Uncertain significance (Jul 12, 2022)
19-2807465-C-A		not specified	Uncertain significance (May 25, 2022)
19-2807489-G-A		not specified	Uncertain significance (Oct 06, 2022)
19-2807498-G-A		not specified	Uncertain significance (Dec 06, 2022)
19-2807507-C-T		not specified	Uncertain significance (Aug 02, 2023)
19-2807508-G-A		not specified	Uncertain significance (Dec 03, 2021)
19-2807522-C-T		not specified	Uncertain significance (Sep 16, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
THOP1	protein_coding	protein_coding	ENST00000307741	13	28142

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000121	1.00	125724	0	21	125745	0.0000835

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.47	372	461	0.807	0.0000330	4480
Missense in Polyphen		146	209.39	0.69728		2028
Synonymous	-0.713	224	211	1.06	0.0000169	1336
Loss of Function	3.09	12	30.4	0.395	0.00000130	367

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000523	0.000511
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000727	0.0000703
Middle Eastern	0.00	0.00
South Asian	0.0000340	0.0000327
Other	0.000168	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in the metabolism of neuropeptides under 20 amino acid residues long. Involved in cytoplasmic peptide degradation. Able to degrade the amyloid-beta precursor protein and generate amyloidogenic fragments.
• Pathway: Renin-angiotensin system - Homo sapiens (human);African trypanosomiasis - Homo sapiens (human) (Consensus)

Recessive Scores

• pRec: 0.174

Intolerance Scores

• loftool: 0.583
• rvis_EVS: -1.48
• rvis_percentile_EVS: 3.7

Haploinsufficiency Scores

• pHI: 0.0856
• hipred: N
• hipred_score: 0.448
• ghis: 0.606

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.935

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Thop1

Gene ontology

• Biological process: protein polyubiquitination;proteolysis;peptide metabolic process
• Cellular component: mitochondrial intermembrane space;cytosol
• Molecular function: metalloendopeptidase activity;peptide binding;metal ion binding