TOR1B

torsin family 1 member B, the group of Torsins

Basic information

Region (hg38): 9:129803157-129811281

Links

ENSG00000136816 ∙ NCBI:27348 ∙ OMIM:608050 ∙ HGNC:11995 ∙ Uniprot:O14657 ∙ 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 TOR1B gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TOR1B 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			18			18
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	18	0	1

Variants in TOR1B

This is a list of pathogenic ClinVar variants found in the TOR1B region.

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

Position	Type	Phenotype	Significance	ClinVar
9-129803219-C-T		not specified	Uncertain significance (Apr 17, 2024)
9-129803276-G-C		not specified	Uncertain significance (Jan 31, 2024)
9-129803346-C-T		not specified	Uncertain significance (Apr 23, 2024)
9-129803354-G-A		not specified	Uncertain significance (Mar 11, 2024)
9-129803397-C-T		not specified	Uncertain significance (Aug 04, 2023)
9-129803405-G-A		not specified	Uncertain significance (Dec 09, 2023)
9-129804184-C-T		not specified	Uncertain significance (Nov 09, 2022)
9-129804214-G-A		not specified	Uncertain significance (Apr 24, 2024)
9-129804323-G-T		not specified	Uncertain significance (Dec 28, 2022)
9-129807198-A-G		not specified	Uncertain significance (Jan 08, 2024)
9-129807253-C-T			Benign (Aug 06, 2018)
9-129807264-A-C		not specified	Uncertain significance (Sep 26, 2023)
9-129807273-C-T		not specified	Uncertain significance (Jul 14, 2023)
9-129807282-T-C		not specified	Uncertain significance (Nov 21, 2023)
9-129807302-C-A		not specified	Uncertain significance (Jun 23, 2023)
9-129807314-G-A		not specified	Uncertain significance (Sep 27, 2021)
9-129807326-G-A		not specified	Uncertain significance (Jun 03, 2022)
9-129808934-C-T		not specified	Uncertain significance (Apr 04, 2024)
9-129808942-G-T		not specified	Uncertain significance (Nov 10, 2022)
9-129809020-A-G		not specified	Uncertain significance (May 02, 2024)
9-129809021-A-G		not specified	Uncertain significance (Oct 21, 2021)
9-129809475-A-T		not specified	Uncertain significance (Dec 13, 2023)
9-129809488-A-G		not specified	Uncertain significance (Dec 08, 2023)
9-129809566-C-T		not specified	Uncertain significance (Feb 28, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TOR1B	protein_coding	protein_coding	ENST00000259339	5	8129

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0642	0.922	125716	0	32	125748	0.000127

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.958	157	195	0.807	0.0000110	2196
Missense in Polyphen		17	33.971	0.50043		423
Synonymous	0.835	74	83.7	0.884	0.00000522	660
Loss of Function	2.15	4	12.1	0.332	5.15e-7	147

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000351	0.000351
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000797	0.0000791
Middle Eastern	0.000109	0.000109
South Asian	0.000294	0.000294
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May serve as a molecular chaperone assisting in the proper folding of secreted and/or membrane proteins. Plays a role in non-neural cells nuclear envelope and endoplasmic reticulum integrity. May have a redundant function with TOR1A in non-neural tissues. {ECO:0000269|PubMed:23569223, ECO:0000269|PubMed:24275647}.
• Pathway: Vesicle-mediated transport;Membrane Trafficking;Clathrin-mediated endocytosis;Cargo recognition for clathrin-mediated endocytosis (Consensus)

Recessive Scores

• pRec: 0.153

Intolerance Scores

• loftool: 0.473
• rvis_EVS: -0.6
• rvis_percentile_EVS: 17.75

Haploinsufficiency Scores

• pHI: 0.155
• hipred: N
• hipred_score: 0.497
• ghis: 0.553

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.901

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tor1b

Gene ontology

• Biological process: response to unfolded protein;endoplasmic reticulum organization;chaperone cofactor-dependent protein refolding;protein homooligomerization;nuclear membrane organization
• Cellular component: nuclear envelope;endoplasmic reticulum;endoplasmic reticulum lumen;nuclear membrane;extracellular exosome
• Molecular function: protein binding;ATP binding;ATPase activity