STH

saitohin

Basic information

Region (hg38): 17:45999250-45999694

Links

ENSG00000256762 ∙ NCBI:246744 ∙ OMIM:607067 ∙ HGNC:18839 ∙ Uniprot:Q8IWL8 ∙ 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 STH gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the STH 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			6	3		9
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	6	3	0

Variants in STH

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

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

Position	Type	Phenotype	Significance	ClinVar
17-45999284-G-T		not specified	Uncertain significance (Feb 09, 2022)
17-45999342-G-T		not specified	Uncertain significance (Nov 09, 2023)
17-45999344-C-T		not specified	Uncertain significance (Oct 22, 2021)
17-45999353-T-C		not specified	Likely benign (Mar 16, 2022)
17-45999360-C-T		EBV-positive nodal T- and NK-cell lymphoma	Likely benign (-)
17-45999396-G-T		not specified	Uncertain significance (Mar 07, 2025)
17-45999473-T-C		not specified	Uncertain significance (Oct 22, 2021)
17-45999535-A-G		not specified	Likely benign (Jul 25, 2023)
17-45999605-C-G		not specified	Uncertain significance (Feb 11, 2025)
17-45999614-C-A		not specified	Uncertain significance (Nov 08, 2021)
17-45999634-G-C		not specified	Uncertain significance (Oct 06, 2023)
17-45999647-C-T		not specified	Likely benign (Aug 23, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
STH	protein_coding	protein_coding	ENST00000537309	1	445

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.143	63	66.3	0.950	0.00000306	814
Missense in Polyphen		6	8.7586	0.68504		74
Synonymous	1.65	16	26.9	0.595	0.00000130	268
Loss of Function

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish
East Asian
Finnish
European (Non-Finnish)
Middle Eastern
South Asian
Other

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.727
• rvis_EVS: 0.66
• rvis_percentile_EVS: 84.27

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.146
• ghis: 0.403

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Gene ontology

• Biological process: positive regulation of mRNA splicing, via spliceosome
• Cellular component: nucleus;cytoplasm;perinuclear region of cytoplasm
• Molecular function: protein binding