TOR2A

torsin family 2 member A, the group of Torsins

Basic information

Region (hg38): 9:127731524-127735313

Links

ENSG00000160404 ∙ NCBI:27433 ∙ OMIM:608052 ∙ HGNC:11996 ∙ Uniprot:Q5JU69, Q8N2E6 ∙ 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 TOR2A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TOR2A 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				5		5
missense			34	2	1	37
nonsense				1		1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	34	8	1

Variants in TOR2A

This is a list of pathogenic ClinVar variants found in the TOR2A region.

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

Position	Type	Phenotype	Significance	ClinVar
9-127732042-A-G		not specified	Uncertain significance (Oct 02, 2023)
9-127732048-C-T		not specified	Likely benign (Dec 23, 2024)
9-127732053-C-T		not specified	Uncertain significance (Jul 30, 2024)
9-127732056-G-A		not specified	Uncertain significance (May 10, 2024)
9-127732063-C-T		not specified	Uncertain significance (Jan 26, 2022)
9-127732075-C-T		not specified	Uncertain significance (Dec 13, 2022)
9-127732093-G-T			Benign (Jun 21, 2018)
9-127732175-C-T		not specified	Likely benign (May 20, 2024)
9-127732187-G-A		not specified	Likely benign (Jun 07, 2024)
9-127732195-G-A		not specified	Uncertain significance (Mar 27, 2023)
9-127732199-G-A		not specified	Likely benign (Sep 26, 2023)
9-127732215-G-A		not specified	Uncertain significance (Jul 31, 2024)
9-127732215-G-C		not specified	Uncertain significance (Apr 08, 2022)
9-127732223-G-T		not specified	Likely benign (Jan 29, 2025)
9-127732234-C-T		not specified	Uncertain significance (May 24, 2023)
9-127732235-G-A		not specified	Likely benign (Jun 23, 2023)
9-127732255-T-C		not specified	Uncertain significance (Jun 30, 2024)
9-127732263-G-A		not specified	Uncertain significance (May 13, 2024)
9-127732266-T-C		not specified	Uncertain significance (Jul 21, 2021)
9-127732588-G-A		not specified	Uncertain significance (Mar 02, 2023)
9-127732606-G-C		not specified	Uncertain significance (Jan 04, 2024)
9-127732629-C-G		not specified	Uncertain significance (Jul 30, 2024)
9-127732639-G-A		not specified	Uncertain significance (Jan 21, 2025)
9-127732650-G-A		not specified	Uncertain significance (Jan 23, 2025)
9-127732657-A-T		not specified	Uncertain significance (Sep 01, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TOR2A	protein_coding	protein_coding	ENST00000373284	5	3802

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.136	0.845	125661	1	8	125670	0.0000358

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.247	181	191	0.950	0.0000128	2037
Missense in Polyphen		70	67.359	1.0392		741
Synonymous	0.167	85	87.0	0.977	0.00000587	694
Loss of Function	2.03	3	9.90	0.303	4.23e-7	120

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000123	0.000120
Ashkenazi Jewish	0.000200	0.0000993
East Asian	0.0000560	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000268	0.0000264
Middle Eastern	0.0000560	0.0000544
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Salusins -alpha and -beta may be endocrine and/or paracrine factors able to increase intracellular calcium concentrations and induce cell mitogenesis. Salusins may also be potent hypotensive peptides. {ECO:0000269|PubMed:12910263}.

Recessive Scores

• pRec: 0.107

Intolerance Scores

• loftool: 0.491
• rvis_EVS: 0.6
• rvis_percentile_EVS: 82.66

Haploinsufficiency Scores

• pHI: 0.122
• hipred: N
• hipred_score: 0.219
• ghis: 0.427

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.471

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tor2a

Gene ontology

• Biological process: chaperone cofactor-dependent protein refolding;protein homooligomerization
• Cellular component: endoplasmic reticulum lumen
• Molecular function: ATP binding