TOR4A

torsin family 4 member A, the group of Torsins

Basic information

Region (hg38): 9:137277725-137282641

Previous symbols: [ "C9orf167" ]

Links

ENSG00000198113 ∙ NCBI:54863 ∙ ∙ HGNC:25981 ∙ Uniprot:Q9NXH8 ∙ 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 TOR4A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TOR4A 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				3		3
missense			35	3		38
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	35	6	0

Variants in TOR4A

This is a list of pathogenic ClinVar variants found in the TOR4A region.

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

Position	Type	Phenotype	Significance	ClinVar
9-137278727-C-T		not specified	Uncertain significance (Nov 12, 2021)
9-137278768-C-A		not specified	Uncertain significance (Dec 26, 2023)
9-137278779-C-T			Likely benign (Mar 01, 2022)
9-137278782-C-T			Likely benign (Mar 01, 2022)
9-137278813-C-T		not specified	Uncertain significance (Nov 08, 2022)
9-137278889-C-A		not specified	Uncertain significance (Aug 17, 2022)
9-137278898-A-C		not specified	Uncertain significance (Jul 28, 2021)
9-137278900-C-A		not specified	Uncertain significance (Dec 21, 2023)
9-137278901-T-C		not specified	Uncertain significance (Jan 23, 2024)
9-137278913-A-G		not specified	Uncertain significance (Oct 26, 2021)
9-137278945-C-A		not specified	Uncertain significance (Mar 06, 2023)
9-137278945-C-T		not specified	Likely benign (Nov 17, 2023)
9-137278946-C-T		not specified	Uncertain significance (May 02, 2024)
9-137279009-G-C		not specified	Uncertain significance (Jan 31, 2024)
9-137279116-G-A		not specified	Uncertain significance (Aug 02, 2021)
9-137279126-A-G		not specified	Uncertain significance (Jun 23, 2023)
9-137279140-G-C		not specified	Uncertain significance (Dec 28, 2022)
9-137279204-T-C		not specified	Uncertain significance (Jun 24, 2022)
9-137279230-A-C		not specified	Uncertain significance (Dec 06, 2022)
9-137279257-C-A		not specified	Uncertain significance (Dec 07, 2023)
9-137279263-C-G		not specified	Uncertain significance (Aug 21, 2023)
9-137279326-T-C		not specified	Uncertain significance (Jan 24, 2023)
9-137279329-G-A		not specified	Uncertain significance (Aug 31, 2022)
9-137279340-C-G		not specified	Uncertain significance (Aug 19, 2023)
9-137279350-G-A		not specified	Uncertain significance (Sep 17, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TOR4A	protein_coding	protein_coding	ENST00000357503	1	4893

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.561	0.428	120486	0	2	120488	0.00000830

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.92	159	302	0.527	0.0000256	2577
Missense in Polyphen		32	79.914	0.40043		701
Synonymous	1.49	131	155	0.848	0.0000140	961
Loss of Function	2.04	1	6.68	0.150	3.14e-7	75

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000204	0.0000185
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Pathway: Platelet degranulation ;Response to elevated platelet cytosolic Ca2+;Platelet activation, signaling and aggregation;Hemostasis (Consensus)

Recessive Scores

• pRec: 0.121

Haploinsufficiency Scores

• pHI: 0.0900
• hipred: N
• hipred_score: 0.459
• ghis: 0.491

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: K

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tor4a

Gene ontology

• Biological process: platelet degranulation
• Cellular component: extracellular region;integral component of membrane;platelet alpha granule lumen
• Molecular function: ATP binding