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.

• not_specified (60 variants)
• not_provided (2 variants)

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. These statistics are base on transcript: NM_001085347.3. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				7		7
missense			51	2	1	54
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	51	9	1

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