TOR3A

torsin family 3 member A, the group of Torsins|Minor histocompatibility antigens

Basic information

Region (hg38): 1:179082070-179098023

Previous symbols: [ "ADIR" ]

Links

ENSG00000186283 ∙ NCBI:64222 ∙ OMIM:607555 ∙ HGNC:11997 ∙ Uniprot:Q9H497 ∙ 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 TOR3A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TOR3A 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			29	2		31
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	29	3	0

Variants in TOR3A

This is a list of pathogenic ClinVar variants found in the TOR3A region.

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

Position	Type	Phenotype	Significance	ClinVar
1-179082181-C-G		not specified	Uncertain significance (Nov 09, 2021)
1-179082204-G-A		not specified	Likely benign (Feb 17, 2022)
1-179082247-G-C		not specified	Uncertain significance (Nov 08, 2022)
1-179082295-G-C		not specified	Uncertain significance (Dec 20, 2023)
1-179082333-C-G		not specified	Uncertain significance (Aug 22, 2023)
1-179082361-A-T		not specified	Uncertain significance (Nov 09, 2023)
1-179082369-G-A		not specified	Uncertain significance (Dec 28, 2022)
1-179082978-C-T		not specified	Uncertain significance (Nov 08, 2022)
1-179083023-G-A		not specified	Uncertain significance (Jun 11, 2024)
1-179085745-C-T		not specified	Uncertain significance (Dec 15, 2022)
1-179085780-G-A		not specified	Uncertain significance (Oct 03, 2022)
1-179085796-T-C		not specified	Likely benign (May 14, 2024)
1-179085826-G-C		not specified	Uncertain significance (Feb 27, 2023)
1-179085842-G-T		not specified	Uncertain significance (Feb 06, 2023)
1-179087932-C-T		not specified	Uncertain significance (Apr 24, 2023)
1-179087933-G-C		not specified	Uncertain significance (Aug 02, 2021)
1-179087935-G-C		not specified	Uncertain significance (Sep 17, 2021)
1-179087939-C-T		not specified	Uncertain significance (Apr 25, 2023)
1-179087953-C-T		not specified	Uncertain significance (Oct 05, 2023)
1-179088008-A-G		not specified	Uncertain significance (Jul 26, 2022)
1-179088013-C-T		not specified	Uncertain significance (Mar 21, 2023)
1-179088031-C-T		not specified	Uncertain significance (Dec 12, 2023)
1-179088088-A-C		not specified	Uncertain significance (Mar 31, 2023)
1-179094094-A-C		not specified	Uncertain significance (Feb 28, 2023)
1-179094170-T-A		not specified	Uncertain significance (Jan 23, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TOR3A	protein_coding	protein_coding	ENST00000367627	6	16647

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.30e-12	0.0188	125468	1	279	125748	0.00111

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.122	204	209	0.976	0.0000121	2543
Missense in Polyphen		64	66.555	0.96161		843
Synonymous	-0.670	97	89.0	1.09	0.00000506	769
Loss of Function	-0.357	17	15.5	1.10	6.67e-7	187

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00360	0.00354
Ashkenazi Jewish	0.000101	0.0000992
East Asian	0.00324	0.00310
Finnish	0.0000464	0.0000462
European (Non-Finnish)	0.000735	0.000721
Middle Eastern	0.00324	0.00310
South Asian	0.00239	0.00239
Other	0.000824	0.000815

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0955

Intolerance Scores

• loftool: 0.868
• rvis_EVS: -0.49
• rvis_percentile_EVS: 22.51

Haploinsufficiency Scores

• pHI: 0.0619
• hipred: N
• hipred_score: 0.170
• ghis: 0.551

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tor3a

Gene ontology

• Cellular component: endoplasmic reticulum;endoplasmic reticulum lumen;extracellular exosome
• Molecular function: ATP binding;ATPase activity