STON1

stonin 1

Basic information

Region (hg38): 2:48529382-48598513

Links

ENSG00000243244 ∙ NCBI:11037 ∙ OMIM:605357 ∙ HGNC:17003 ∙ Uniprot:Q9Y6Q2 ∙ 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 STON1 gene.

• not provided (1 variants)
• Inborn genetic diseases (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the STON1 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			1		1	2
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	1	0	1

Variants in STON1

This is a list of pathogenic ClinVar variants found in the STON1 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-48580809-G-A		not specified	Uncertain significance (May 11, 2022)
2-48580986-G-T			Benign (Dec 13, 2017)
2-48582194-T-C		not specified	Uncertain significance (Feb 14, 2024)
2-48591794-G-T		Myoepithelial tumor	Uncertain significance (Nov 01, 2022)
2-48595258-G-A		not specified	Uncertain significance (Jan 30, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
STON1	protein_coding	protein_coding	ENST00000309835	3	69504

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.49e-11	0.343	124658	0	157	124815	0.000629

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-2.51	491	357	1.37	0.0000172	4780
Missense in Polyphen		192	127.26	1.5087		1708
Synonymous	-1.13	150	133	1.12	0.00000655	1395
Loss of Function	1.08	20	25.9	0.771	0.00000135	347

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000828	0.000828
Ashkenazi Jewish	0.00202	0.00179
East Asian	0.00147	0.00147
Finnish	0.00	0.00
European (Non-Finnish)	0.000615	0.000608
Middle Eastern	0.00147	0.00147
South Asian	0.000638	0.000621
Other	0.000828	0.000816

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved in the endocytic machinery. {ECO:0000250}.
• Pathway: Vesicle-mediated transport;Membrane Trafficking;Clathrin-mediated endocytosis;Cargo recognition for clathrin-mediated endocytosis (Consensus)

Recessive Scores

• pRec: 0.104

Intolerance Scores

• loftool: 0.970
• rvis_EVS: 1.61
• rvis_percentile_EVS: 95.91

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.112
• ghis: 0.531

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.260

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ston1
• Phenotype: cellular phenotype

Gene ontology

• Biological process: endocytosis;regulation of endocytosis
• Cellular component: cytoplasm;membrane