ST8SIA6

ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 6, the group of Sialyltransferases

Basic information

Region (hg38): 10:17315421-17454595

Previous symbols: [ "SIAT8F" ]

Links

ENSG00000148488 ∙ NCBI:338596 ∙ OMIM:610139 ∙ HGNC:23317 ∙ Uniprot:P61647 ∙ 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 ST8SIA6 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ST8SIA6 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			16			16
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	16	0	0

Variants in ST8SIA6

This is a list of pathogenic ClinVar variants found in the ST8SIA6 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-17320926-G-T		not specified	Uncertain significance (Jun 07, 2023)
10-17320958-G-A		not specified	Uncertain significance (Mar 16, 2024)
10-17321014-G-T		not specified	Uncertain significance (Mar 15, 2024)
10-17321030-T-G		not specified	Uncertain significance (Oct 03, 2023)
10-17321063-C-T		not specified	Uncertain significance (Oct 01, 2024)
10-17321067-T-G		not specified	Uncertain significance (Nov 08, 2022)
10-17321105-C-T		not specified	Uncertain significance (Dec 06, 2022)
10-17321122-G-A		not specified	Uncertain significance (Jan 04, 2024)
10-17321132-C-T		not specified	Uncertain significance (Jun 06, 2023)
10-17321169-C-A		not specified	Uncertain significance (May 15, 2023)
10-17321185-A-T		not specified	Uncertain significance (Jun 22, 2021)
10-17321198-T-C		not specified	Uncertain significance (Sep 26, 2024)
10-17321213-C-T		not specified	Likely benign (Aug 12, 2024)
10-17321311-A-T		not specified	Uncertain significance (Jun 25, 2024)
10-17323090-T-A		not specified	Uncertain significance (Apr 15, 2024)
10-17331428-T-C		not specified	Uncertain significance (Sep 17, 2021)
10-17331430-T-A		not specified	Uncertain significance (Dec 10, 2024)
10-17331496-T-C		not specified	Uncertain significance (Sep 29, 2023)
10-17331526-G-A		not specified	Uncertain significance (Feb 05, 2024)
10-17359547-C-A		Malignant tumor of prostate	Uncertain significance (-)
10-17359589-T-G		not specified	Uncertain significance (Jan 30, 2024)
10-17390597-A-C		not specified	Uncertain significance (Mar 27, 2023)
10-17390609-T-G		not specified	Uncertain significance (Jun 16, 2023)
10-17453563-T-A		not specified	Uncertain significance (Mar 12, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ST8SIA6	protein_coding	protein_coding	ENST00000377602	8	135948

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
7.16e-10	0.0756	125719	0	28	125747	0.000111

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.431	199	183	1.09	0.00000927	2589
Missense in Polyphen		70	66.272	1.0563		842
Synonymous	-1.15	86	73.5	1.17	0.00000429	771
Loss of Function	-0.0297	14	13.9	1.01	5.86e-7	208

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000211	0.000211
Ashkenazi Jewish	0.000104	0.0000992
East Asian	0.000225	0.000217
Finnish	0.00	0.00
European (Non-Finnish)	0.0000725	0.0000703
Middle Eastern	0.000225	0.000217
South Asian	0.000338	0.000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Prefers O-glycans to N-glycans or glycolipids as acceptor substrates. The minimal acceptor substrate is the NeuAc- alpha-2,3(6)-Gal sequence at the non-reducing end of their carbohydrate groups (By similarity). {ECO:0000250}.
• Pathway: Post-translational protein modification;N-Glycan antennae elongation;N-glycan antennae elongation in the medial/trans-Golgi;Metabolism of proteins;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 (Consensus)

Recessive Scores

• pRec: 0.115

Intolerance Scores

• loftool: 0.859
• rvis_EVS: 0.2
• rvis_percentile_EVS: 67.19

Haploinsufficiency Scores

• pHI: 0.0743
• hipred: N
• hipred_score: 0.264
• ghis: 0.384

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.317

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: St8sia6

Zebrafish Information Network

• Gene name: st8sia6
• Affected structure: olfactory bulb glomerulus
• Phenotype tag: abnormal
• Phenotype quality: aplastic/hypoplastic

Gene ontology

• Biological process: ganglioside biosynthetic process;blastocyst hatching;protein O-linked glycosylation;glycoprotein metabolic process;glycolipid biosynthetic process;oligosaccharide metabolic process;carbohydrate biosynthetic process;sialylation
• Cellular component: Golgi membrane;integral component of membrane
• Molecular function: alpha-N-acetylneuraminate alpha-2,8-sialyltransferase activity;sialyltransferase activity