STON2

stonin 2

Basic information

Region (hg38): 14:81260651-81436465

Links

ENSG00000140022 ∙ NCBI:85439 ∙ OMIM:608467 ∙ HGNC:30652 ∙ Uniprot:Q8WXE9 ∙ 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 STON2 gene.

• Inborn genetic diseases (31 variants)
• not provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the STON2 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			26	2		28
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding			1	2		3
Total	0	0	27	5	0

Variants in STON2

This is a list of pathogenic ClinVar variants found in the STON2 region.

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

Position	Type	Phenotype	Significance	ClinVar
14-81270573-C-G		not specified	Uncertain significance (Jun 02, 2023)
14-81270579-T-C		not specified	Likely benign (Jan 03, 2022)
14-81270600-A-G		not specified	Likely benign (Mar 21, 2023)
14-81270735-T-C		not specified	Uncertain significance (Jul 15, 2021)
14-81270797-T-C		not specified	Likely benign (Mar 29, 2022)
14-81276940-T-G		not specified	Uncertain significance (Jan 30, 2024)
14-81277056-G-T		not specified	Uncertain significance (Feb 10, 2022)
14-81277059-T-G		not specified	Uncertain significance (Jul 12, 2022)
14-81277062-T-C		not specified	Uncertain significance (Aug 11, 2022)
14-81277078-C-G		not specified	Uncertain significance (Jun 22, 2023)
14-81277081-T-C		not specified	Uncertain significance (Oct 27, 2023)
14-81277105-T-C		not specified	Uncertain significance (Jan 24, 2023)
14-81277120-G-A		not specified	Uncertain significance (Jul 09, 2021)
14-81277153-G-C		not specified	Uncertain significance (Apr 07, 2022)
14-81277168-C-T		not specified	Uncertain significance (Feb 27, 2024)
14-81277171-A-C		not specified	Uncertain significance (Dec 14, 2021)
14-81277197-C-G		not specified	Uncertain significance (Sep 22, 2022)
14-81277236-G-A		not specified	Uncertain significance (Jan 30, 2024)
14-81277305-G-A		not specified	Uncertain significance (Jan 05, 2022)
14-81277338-T-C		not specified	Likely benign (Feb 17, 2023)
14-81277417-T-C		not specified	Uncertain significance (Jan 03, 2024)
14-81277518-C-T		not specified	Uncertain significance (Sep 27, 2021)
14-81277544-C-A		not specified	Uncertain significance (Jul 06, 2021)
14-81277755-G-C		not specified	Uncertain significance (Jan 18, 2022)
14-81277857-G-A		not specified	Uncertain significance (Nov 15, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
STON2	protein_coding	protein_coding	ENST00000555447	6	175810

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000165	0.999	125661	0	87	125748	0.000346

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.251	485	501	0.968	0.0000283	6082
Missense in Polyphen		181	188.19	0.96177		2338
Synonymous	-0.361	200	194	1.03	0.0000108	1828
Loss of Function	2.83	11	26.8	0.411	0.00000125	324

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000514	0.000514
Ashkenazi Jewish	0.000298	0.000198
East Asian	0.000490	0.000489
Finnish	0.000139	0.000139
European (Non-Finnish)	0.000485	0.000484
Middle Eastern	0.000490	0.000489
South Asian	0.000170	0.000163
Other	0.000326	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Adapter protein involved in endocytic machinery. Involved in the synaptic vesicle recycling. May facilitate clathrin-coated vesicle uncoating. {ECO:0000269|PubMed:11381094, ECO:0000269|PubMed:11454741, ECO:0000269|PubMed:21102408}.
• Pathway: Vesicle-mediated transport;Membrane Trafficking;Clathrin-mediated endocytosis;Cargo recognition for clathrin-mediated endocytosis (Consensus)

Recessive Scores

• pRec: 0.0968

Intolerance Scores

• loftool: 0.578
• rvis_EVS: -0.41
• rvis_percentile_EVS: 25.84

Haploinsufficiency Scores

• pHI: 0.0509
• hipred: Y
• hipred_score: 0.808
• ghis: 0.514

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.488

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	High	High	High
Primary Immunodeficiency	High	High	High
Cancer	High	High	High

Mouse Genome Informatics

• Gene name: Ston2
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan)

Gene ontology

• Biological process: hematopoietic progenitor cell differentiation;regulation of endocytosis;synaptic vesicle endocytosis;membrane organization
• Cellular component: nucleolus;cytosol;synaptic vesicle;membrane;cell junction;clathrin-coated vesicle;neuron projection
• Molecular function: protein binding