STON1-GTF2A1L

STON1-GTF2A1L readthrough

Basic information

Region (hg38): 2:48529924-48776517

Links

ENSG00000068781 ∙ NCBI:286749 ∙ ∙ HGNC:30651 ∙ ∙ ∙ 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-GTF2A1L gene.

• Inborn genetic diseases (3 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the STON1-GTF2A1L 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			2		1	3
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	3	0	1

Variants in STON1-GTF2A1L

This is a list of pathogenic ClinVar variants found in the STON1-GTF2A1L 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)
2-48617882-G-C		not specified	Uncertain significance (May 04, 2022)
2-48620875-G-C		not specified	Uncertain significance (Aug 12, 2021)
2-48620897-G-A		not specified	Uncertain significance (Feb 28, 2024)
2-48621216-G-A		not specified	Uncertain significance (Apr 08, 2022)
2-48621265-G-C		not specified	Uncertain significance (Sep 06, 2022)
2-48646457-C-G		not specified	Uncertain significance (Oct 29, 2021)
2-48646471-A-G		not specified	Uncertain significance (Aug 02, 2022)
2-48646471-A-T		not specified	Uncertain significance (Dec 23, 2022)
2-48646512-A-G		not specified	Uncertain significance (Dec 08, 2023)
2-48646525-C-T		not specified	Uncertain significance (Jul 19, 2022)
2-48646611-A-G		not specified	Uncertain significance (Sep 15, 2021)
2-48646648-A-G		not specified	Uncertain significance (Sep 17, 2021)
2-48646651-A-C		not specified	Uncertain significance (Jan 19, 2024)
2-48646656-G-A		not specified	Likely benign (Dec 07, 2021)
2-48646657-C-T		not specified	Uncertain significance (May 25, 2022)
2-48646675-C-T		not specified	Uncertain significance (Dec 03, 2021)
2-48646717-T-C		not specified	Uncertain significance (Sep 14, 2022)
2-48646723-C-T		not specified	Uncertain significance (Aug 12, 2021)
2-48646731-A-G		not specified	Uncertain significance (May 16, 2023)
2-48646771-A-G		not specified	Uncertain significance (Mar 04, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
STON1-GTF2A1L	protein_coding	protein_coding	ENST00000394754	10	246591

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.52e-22	0.0180	124654	0	228	124882	0.000913

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-2.79	779	589	1.32	0.0000282	7732
Missense in Polyphen		298	241.07	1.2361		3293
Synonymous	-2.44	262	216	1.21	0.0000109	2255
Loss of Function	1.03	38	45.5	0.835	0.00000225	594

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00211	0.00211
Ashkenazi Jewish	0.00202	0.00179
East Asian	0.00234	0.00234
Finnish	0.00	0.00
European (Non-Finnish)	0.000818	0.000803
Middle Eastern	0.00234	0.00234
South Asian	0.000770	0.000752
Other	0.00117	0.00114

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)

Intolerance Scores

• rvis_EVS: 1.24
• rvis_percentile_EVS: 93.31

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.139

Essentials

• essential_gene_CRISPR: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.106

Gene Damage Prediction

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

Gene ontology

• Biological process: transcription by RNA polymerase II;transcription initiation from RNA polymerase II promoter;endocytosis;regulation of endocytosis
• Cellular component: transcription factor TFIIA complex;membrane