STOX1

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Basic information

Region (hg38): 10:68827531-68895432

Previous symbols: [ "C10orf24" ]

Links

ENSG00000165730 ∙ NCBI:219736 ∙ OMIM:609397 ∙ HGNC:23508 ∙ Uniprot:Q6ZVD7 ∙ 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 STOX1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the STOX1 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				5	2	7
missense			49	5	3	57
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding				1		1
Total	0	0	49	11	5

Variants in STOX1

This is a list of pathogenic ClinVar variants found in the STOX1 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-68827661-C-A		not specified	Uncertain significance (Oct 12, 2021)
10-68827676-G-C			Benign (Jul 01, 2024)
10-68827694-C-G		not specified	Uncertain significance (Jul 22, 2022)
10-68827699-G-A		not specified	Uncertain significance (Nov 30, 2022)
10-68827726-G-T		not specified	Uncertain significance (Dec 14, 2022)
10-68827727-C-T		not specified	Uncertain significance (Dec 14, 2022)
10-68827735-C-T		not specified	Uncertain significance (Jun 03, 2022)
10-68827757-C-G		not specified	Uncertain significance (Dec 19, 2022)
10-68827772-A-C		not specified	Uncertain significance (Jan 22, 2024)
10-68827783-G-A		not specified	Uncertain significance (Jan 08, 2024)
10-68827786-C-G		not specified	Uncertain significance (Mar 31, 2024)
10-68827801-C-T			Likely benign (Mar 01, 2023)
10-68827808-T-C		not specified	Uncertain significance (Jul 30, 2024)
10-68827818-G-C		not specified	Uncertain significance (Nov 19, 2022)
10-68827826-G-C		not specified	Uncertain significance (Mar 01, 2024)
10-68827828-G-A		not specified	Uncertain significance (Apr 06, 2024)
10-68827831-G-A		not specified	Uncertain significance (Sep 08, 2024)
10-68827832-T-C		not specified	Uncertain significance (Jun 19, 2024)
10-68827844-G-A		not specified	Likely benign (Sep 27, 2024)
10-68827849-C-A		not specified	Uncertain significance (May 30, 2024)
10-68827849-C-T		not specified	Uncertain significance (Jun 28, 2024)
10-68827853-C-T		not specified	Uncertain significance (Dec 07, 2024)
10-68827868-T-C		not specified	Uncertain significance (May 31, 2023)
10-68828137-C-T			Likely benign (Mar 01, 2023)
10-68882090-G-A		not specified	Likely benign (Jul 10, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
STOX1	protein_coding	protein_coding	ENST00000298596	4	67891

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.44e-16	0.0829	124777	0	15	124792	0.0000601

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.336	438	458	0.956	0.0000235	6502
Missense in Polyphen		94	99.141	0.94815		1621
Synonymous	-0.0254	168	168	1.00	0.00000899	1935
Loss of Function	0.974	28	34.1	0.820	0.00000216	428

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.000389	0.000389
Finnish	0.00	0.00
European (Non-Finnish)	0.0000628	0.0000618
Middle Eastern	0.000389	0.000389
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in regulating the levels of reactive oxidative species and reactive nitrogen species and in mitochondrial homeostasis in the placenta (PubMed:24738702). Required for regulation of inner ear epithelial cell proliferation via the AKT signaling pathway (By similarity). {ECO:0000250|UniProtKB:B2RQL2, ECO:0000269|PubMed:24738702}.

Recessive Scores

• pRec: 0.106

Intolerance Scores

• loftool: 0.645
• rvis_EVS: 1.45
• rvis_percentile_EVS: 95.14

Haploinsufficiency Scores

• pHI: 0.0916
• hipred: N
• hipred_score: 0.212
• ghis: 0.411

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.122

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Stox1

Gene ontology

• Biological process: cell cycle;positive regulation of cell population proliferation;regulation of gene expression;positive regulation of gene expression;negative regulation of gene expression;positive regulation of peptidyl-threonine phosphorylation;regulation of mitochondrion organization;positive regulation of G2/M transition of mitotic cell cycle;positive regulation of peptidyl-serine phosphorylation;inner ear development;positive regulation of epithelial cell proliferation;cell division;regulation of mitochondrial membrane potential;positive regulation of protein kinase B signaling;regulation of transcription from RNA polymerase II promoter in response to hypoxia;cellular response to nitrosative stress;regulation of mitochondrial DNA metabolic process;regulation of response to oxidative stress;positive regulation of cyclin-dependent protein kinase activity;positive regulation of otic vesicle morphogenesis
• Cellular component: fibrillar center;nucleus;nucleoplasm;cytoplasm;centrosome;cytosol;cell cortex
• Molecular function: RNA polymerase II regulatory region sequence-specific DNA binding;protein binding