STON2

stonin 2

Basic information

Region (hg38): 14:81260652-81436465

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.

• not_specified (83 variants)
• not_provided (3 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. These statistics are base on transcript: NM_001394390.1. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				1		1
missense			75	3	1	79
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	75	4	1

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