CASTOR1

cytosolic arginine sensor for mTORC1 subunit 1

Basic information

Region (hg38): 22:30285117-30289622

Previous symbols: [ "GATSL3" ]

Links

ENSG00000239282 ∙ NCBI:652968 ∙ OMIM:617034 ∙ HGNC:34423 ∙ Uniprot:Q8WTX7 ∙ 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 CASTOR1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CASTOR1 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			25			25
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	25	0	0

Variants in CASTOR1

This is a list of pathogenic ClinVar variants found in the CASTOR1 region.

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

Position	Type	Phenotype	Significance	ClinVar
22-30285645-C-T		not specified	Uncertain significance (Jan 09, 2024)
22-30285658-C-G		not specified	Uncertain significance (Sep 29, 2023)
22-30285664-C-T		not specified	Uncertain significance (Dec 16, 2022)
22-30285670-C-T		not specified	Uncertain significance (Jan 18, 2022)
22-30285679-C-T		not specified	Uncertain significance (Jul 09, 2024)
22-30285682-C-T		not specified	Uncertain significance (Oct 04, 2022)
22-30286028-G-A		not specified	Uncertain significance (Jun 21, 2023)
22-30286042-C-T		not specified	Uncertain significance (Feb 21, 2024)
22-30286085-G-A		not specified	Uncertain significance (Mar 09, 2025)
22-30286269-T-C		not specified	Uncertain significance (Jan 02, 2025)
22-30286348-G-C		not specified	Uncertain significance (Mar 19, 2024)
22-30286862-C-T		not specified	Uncertain significance (Aug 17, 2021)
22-30286868-C-T		not specified	Uncertain significance (Dec 28, 2022)
22-30286876-G-A		not specified	Uncertain significance (May 31, 2023)
22-30286918-C-T		not specified	Uncertain significance (Sep 22, 2022)
22-30287157-T-C		not specified	Uncertain significance (Jan 24, 2023)
22-30287200-C-A		not specified	Uncertain significance (Jun 29, 2022)
22-30287227-G-A		not specified	Uncertain significance (Sep 04, 2024)
22-30287253-G-A		not specified	Uncertain significance (Dec 09, 2023)
22-30287266-C-T		not specified	Uncertain significance (Mar 01, 2023)
22-30287384-C-A		not specified	Uncertain significance (Apr 22, 2024)
22-30287398-G-C		not specified	Uncertain significance (Jul 16, 2024)
22-30287449-C-T		not specified	Uncertain significance (Nov 28, 2024)
22-30287477-G-T		not specified	Uncertain significance (Mar 22, 2023)
22-30288735-G-A		not specified	Uncertain significance (Dec 04, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CASTOR1	protein_coding	protein_coding	ENST00000407689	9	4511

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0275	0.962	125041	0	58	125099	0.000232

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.59	140	204	0.686	0.0000123	2099
Missense in Polyphen		42	70.597	0.59492		757
Synonymous	0.912	81	92.1	0.879	0.00000640	682
Loss of Function	2.24	5	14.1	0.355	6.02e-7	162

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000758	0.000667
Ashkenazi Jewish	0.00	0.00
East Asian	0.000172	0.000167
Finnish	0.000245	0.000186
European (Non-Finnish)	0.000303	0.000247
Middle Eastern	0.000172	0.000167
South Asian	0.000192	0.000163
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Functions as an intracellular arginine sensor within the amino acid-sensing branch of the TORC1 signaling pathway. As a homodimer or a heterodimer with CASTOR2, binds and inhibits the GATOR subcomplex GATOR2 and thereby mTORC1. Binding of arginine to CASTOR1 allosterically disrupts the interaction of CASTOR1- containing dimers with GATOR2 which can in turn activate mTORC1 and the TORC1 signaling pathway. {ECO:0000269|PubMed:26972053, ECO:0000269|PubMed:27487210}.

Intolerance Scores

• rvis_EVS: -0.21
• rvis_percentile_EVS: 38.58

Haploinsufficiency Scores

• hipred: Y
• hipred_score: 0.662
• ghis: 0.497

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Castor1
• Phenotype: hematopoietic system phenotype

Gene ontology

• Biological process: regulation of intracellular signal transduction;cellular response to L-arginine;negative regulation of TORC1 signaling
• Cellular component: cytosol;GATOR2 complex
• Molecular function: protein binding;arginine binding;identical protein binding