ST8SIA2

ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 2, the group of Sialyltransferases

Basic information

Region (hg38): 15:92393880-92468728

Previous symbols: [ "SIAT8B" ]

Links

ENSG00000140557 ∙ NCBI:8128 ∙ OMIM:602546 ∙ HGNC:10870 ∙ Uniprot:Q92186 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• schizophrenia (Limited), mode of inheritance: AD

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ST8SIA2 gene.

• Inborn genetic diseases (10 variants)
• not provided (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ST8SIA2 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	2
missense			10			10
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	10	1	1

Variants in ST8SIA2

This is a list of pathogenic ClinVar variants found in the ST8SIA2 region.

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

Position	Type	Phenotype	Significance	ClinVar
15-92438417-C-G		not specified	Uncertain significance (Oct 26, 2022)
15-92438444-G-A		not specified	Uncertain significance (Oct 06, 2021)
15-92438519-C-T		not specified	Uncertain significance (Jun 23, 2023)
15-92438551-G-A		ST8SIA2-related disorder	Likely benign (Sep 25, 2020)
15-92438570-G-A		not specified	Uncertain significance (Jun 24, 2022)
15-92438591-G-T		not specified	Uncertain significance (Jan 03, 2024)
15-92438603-G-A		not specified	Uncertain significance (Sep 27, 2022)
15-92444668-G-A		not specified	Uncertain significance (Mar 21, 2022)
15-92444842-T-C		not specified	Uncertain significance (Jul 20, 2022)
15-92444856-G-A		not specified	Uncertain significance (May 05, 2023)
15-92444926-G-A		not specified	Uncertain significance (May 25, 2022)
15-92464096-C-A			Likely benign (Jul 02, 2018)
15-92464139-C-G		ST8SIA2-related disorder	Likely benign (Apr 29, 2020)
15-92464216-T-C		not specified	Uncertain significance (Mar 20, 2023)
15-92464265-G-T		not specified	Uncertain significance (Oct 05, 2022)
15-92464286-C-T			Benign (Jul 31, 2018)
15-92464292-G-A			Likely benign (Jul 02, 2018)
15-92464367-G-T		ST8SIA2-related disorder	Likely benign (Dec 27, 2022)
15-92464377-G-A		not specified	Uncertain significance (Feb 21, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ST8SIA2	protein_coding	protein_coding	ENST00000268164	6	74901

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0581	0.939	125744	0	4	125748	0.0000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.50	160	223	0.717	0.0000140	2437
Missense in Polyphen		35	84.637	0.41353		913
Synonymous	-1.28	114	97.9	1.16	0.00000672	741
Loss of Function	2.57	5	16.2	0.309	7.63e-7	188

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000264	0.0000264
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May transfer sialic acid through alpha-2,8-linkages to the alpha-2,3-linked and alpha-2,6-linked sialic acid of N-linked oligosaccharides of glycoproteins and may be involved in PSA (polysialic acid) expression.
• Pathway: Developmental Biology;Post-translational protein modification;N-Glycan antennae elongation;N-glycan antennae elongation in the medial/trans-Golgi;Metabolism of proteins;terminal <i>O</i>-glycans residues modification;Sialic acid metabolism;Synthesis of substrates in N-glycan biosythesis;Biosynthesis of the N-glycan precursor (dolichol lipid-linked oligosaccharide, LLO) and transfer to a nascent protein;Transport to the Golgi and subsequent modification;Asparagine N-linked glycosylation;NCAM signaling for neurite out-growth;NCAM1 interactions;Axon guidance (Consensus)

Recessive Scores

• pRec: 0.268

Intolerance Scores

• loftool: 0.155
• rvis_EVS: -0.42
• rvis_percentile_EVS: 25.56

Haploinsufficiency Scores

• pHI: 0.392
• hipred: Y
• hipred_score: 0.851
• ghis: 0.439

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.802

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: St8sia2
• Phenotype: 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); mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); cellular phenotype; growth/size/body region phenotype

Zebrafish Information Network

• Gene name: st8sia2
• Affected structure: diencephalic white matter
• Phenotype tag: abnormal
• Phenotype quality: decreased amount

Gene ontology

• Biological process: ganglioside biosynthetic process;carbohydrate metabolic process;cellular protein modification process;protein glycosylation;N-glycan processing;nervous system development;oligosaccharide metabolic process;sialylation
• Cellular component: Golgi membrane;early endosome;integral component of membrane;recycling endosome
• Molecular function: alpha-N-acetylneuraminate alpha-2,8-sialyltransferase activity;sialic acid binding