TOR1AIP2

torsin 1A interacting protein 2

Basic information

Region (hg38): 1:179839967-179877803

Links

∙ NCBI:163590 ∙ OMIM:614513 ∙ HGNC:24055 ∙ Uniprot:Q8NFQ8, Q9H496 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Muscular dystrophy, limb-girdle, type 2Y	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Cardiovascular; Musculoskeletal	24856141

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the TOR1AIP2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TOR1AIP2 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			2 clinvar	1 clinvar		3
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	2	1	0

Variants in TOR1AIP2

This is a list of pathogenic ClinVar variants found in the TOR1AIP2 region.

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

Position	Phenotype	Significance	ClinVar
1-179850881-C-T	not specified	Likely benign (Jun 22, 2021)	2397151
1-179851097-G-A	not specified	Uncertain significance (Oct 12, 2021)	3181300
1-179851264-G-A	not specified	Uncertain significance (Nov 15, 2021)	2386169

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TOR1AIP2	protein_coding	protein_coding	ENST00000367612	4	37837

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.25e-9	0.176	125732	0	16	125748	0.0000636

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.801	210	245	0.856	0.0000118	3105
Missense in Polyphen		58	89.384	0.64888		1176
Synonymous	-0.174	100	97.8	1.02	0.00000507	923
Loss of Function	0.390	14	15.7	0.894	7.48e-7	195

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.000381	0.000272
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000798	0.0000791
Middle Eastern	0.000381	0.000272
South Asian	0.0000371	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Function: FUNCTION: Required for endoplasmic reticulum integrity. Regulates the distribution of TOR1A between the endoplasmic reticulum and the nuclear envelope as well as induces TOR1A, TOR1B and TOR3A ATPase activity. {ECO:0000269|PubMed:19339278, ECO:0000269|PubMed:23569223, ECO:0000269|PubMed:24275647}.;

Recessive Scores

pRec: 0.0771

Intolerance Scores

loftool: 0.577
rvis_EVS: -0.31
rvis_percentile_EVS: 32.06

Haploinsufficiency Scores

pHI: 0.0764
hipred: N
hipred_score: 0.327
ghis: 0.452

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: S
essential_gene_gene_trap: K
gene_indispensability_pred: N
gene_indispensability_score: 0.223

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Tor1aip2
Phenotype

Gene ontology

Biological process: endoplasmic reticulum organization;positive regulation of ATPase activity;protein localization to nuclear envelope
Cellular component: endoplasmic reticulum;endoplasmic reticulum membrane;integral component of membrane;nuclear membrane
Molecular function: ATPase activator activity;ATPase binding