STOX2

storkhead box 2

Basic information

Region (hg38): 4:183797692-184023526

Links

ENSG00000173320 ∙ NCBI:56977 ∙ OMIM:617359 ∙ HGNC:25450 ∙ Uniprot:Q9P2F5 ∙ 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 STOX2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the STOX2 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			48	2		50
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	48	3	0

Variants in STOX2

This is a list of pathogenic ClinVar variants found in the STOX2 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-183906812-A-G		not specified	Uncertain significance (Dec 21, 2023)
4-183906846-C-T		not specified	Uncertain significance (Sep 22, 2023)
4-183906857-T-G		not specified	Uncertain significance (Dec 14, 2023)
4-183906932-G-C		not specified	Uncertain significance (Dec 19, 2022)
4-184001329-T-G		not specified	Uncertain significance (Apr 25, 2023)
4-184001336-C-G		not specified	Uncertain significance (Mar 31, 2024)
4-184001456-C-T		not specified	Uncertain significance (Oct 10, 2023)
4-184009180-A-T		not specified	Uncertain significance (Nov 09, 2021)
4-184009274-A-G		not specified	Uncertain significance (Aug 12, 2021)
4-184009405-G-T		not specified	Uncertain significance (Sep 06, 2022)
4-184009443-G-A		not specified	Uncertain significance (Nov 07, 2023)
4-184009535-C-A		not specified	Uncertain significance (Feb 09, 2023)
4-184009581-A-G		not specified	Uncertain significance (Feb 15, 2023)
4-184009661-T-G		not specified	Uncertain significance (Jul 26, 2021)
4-184009674-A-G		not specified	Uncertain significance (Jul 19, 2022)
4-184009689-C-G		not specified	Uncertain significance (May 10, 2024)
4-184009736-G-A		not specified	Uncertain significance (Dec 15, 2022)
4-184009800-A-G		not specified	Uncertain significance (May 27, 2022)
4-184009808-G-A		not specified	Uncertain significance (Jul 09, 2021)
4-184009844-A-C		not specified	Uncertain significance (Feb 17, 2022)
4-184009869-G-A		not specified	Uncertain significance (Apr 18, 2023)
4-184009900-C-A		not specified	Uncertain significance (Dec 28, 2023)
4-184010043-C-T		not specified	Uncertain significance (Nov 21, 2023)
4-184010067-G-A		not specified	Uncertain significance (Aug 23, 2021)
4-184010095-T-G		not specified	Uncertain significance (Aug 08, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
STOX2	protein_coding	protein_coding	ENST00000308497	4	170096

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.484	0.516	124589	0	38	124627	0.000152

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.33	446	532	0.838	0.0000312	6067
Missense in Polyphen		138	197.61	0.69834		2220
Synonymous	-0.540	232	222	1.05	0.0000145	1840
Loss of Function	3.84	6	27.8	0.216	0.00000159	348

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000584	0.000582
Ashkenazi Jewish	0.000427	0.000298
East Asian	0.000361	0.000223
Finnish	0.00	0.00
European (Non-Finnish)	0.000177	0.000106
Middle Eastern	0.000361	0.000223
South Asian	0.000256	0.000163
Other	0.000719	0.000496

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.147
• rvis_EVS: -0.17
• rvis_percentile_EVS: 40.65

Haploinsufficiency Scores

• pHI: 0.456
• hipred: Y
• hipred_score: 0.580
• ghis: 0.572

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.307

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Stox2

Gene ontology

• Biological process: maternal placenta development;regulation of transcription by RNA polymerase II;response to bacterium;embryo development ending in birth or egg hatching
• Cellular component: cellular_component
• Molecular function: molecular_function