ST6GALNAC6

ST6 N-acetylgalactosaminide alpha-2,6-sialyltransferase 6, the group of Sialyltransferases

Basic information

Region (hg38): 9:127885321-127905408

Previous symbols: [ "SIAT7F" ]

Links

ENSG00000160408 ∙ NCBI:30815 ∙ OMIM:610135 ∙ HGNC:23364 ∙ Uniprot:Q969X2 ∙ 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 ST6GALNAC6 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ST6GALNAC6 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			19			19
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region			1			1
non coding			1			1
Total	0	0	20	0	0

Variants in ST6GALNAC6

This is a list of pathogenic ClinVar variants found in the ST6GALNAC6 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-127886703-G-A		not specified	Uncertain significance (May 21, 2024)
9-127886777-C-T		not specified	Uncertain significance (Apr 22, 2022)
9-127886792-G-A			Uncertain significance (Jan 01, 2024)
9-127887521-C-T		not specified	Uncertain significance (Jun 30, 2022)
9-127890646-C-T		not specified	Uncertain significance (Nov 29, 2021)
9-127890658-C-T		not specified	Uncertain significance (Oct 30, 2023)
9-127890659-G-A		not specified	Uncertain significance (Dec 03, 2021)
9-127890668-C-T		not specified	Uncertain significance (Apr 08, 2022)
9-127890686-G-A		not specified	Uncertain significance (Aug 22, 2023)
9-127890689-C-T		not specified	Uncertain significance (Aug 09, 2021)
9-127890749-G-A		not specified	Uncertain significance (May 24, 2023)
9-127890784-G-A		not specified	Uncertain significance (Nov 06, 2023)
9-127890820-C-T		not specified	Uncertain significance (Dec 01, 2022)
9-127890940-C-A		not specified	Uncertain significance (Oct 30, 2023)
9-127891033-G-A		not specified	Uncertain significance (Jan 04, 2022)
9-127894577-G-A		not specified	Uncertain significance (Mar 28, 2024)
9-127894670-C-T		not specified	Uncertain significance (Oct 05, 2022)
9-127894685-G-A		not specified	Uncertain significance (Mar 01, 2024)
9-127896252-C-T		not specified	Uncertain significance (Mar 18, 2024)
9-127896268-G-A		not specified	Uncertain significance (Feb 13, 2024)
9-127896270-C-T		not specified	Uncertain significance (Nov 16, 2022)
9-127896279-G-T		not specified	Uncertain significance (Mar 01, 2023)
9-127896315-A-G		not specified	Uncertain significance (Jun 22, 2023)
9-127897971-G-A		not specified	Uncertain significance (Jan 20, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ST6GALNAC6	protein_coding	protein_coding	ENST00000373146	6	20088

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00222	0.981	125736	0	9	125745	0.0000358

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.57	166	233	0.711	0.0000158	2172
Missense in Polyphen		40	81.051	0.49352		788
Synonymous	-0.141	95	93.3	1.02	0.00000616	679
Loss of Function	2.11	7	16.1	0.434	9.41e-7	160

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000292	0.0000292
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000533	0.0000527
Middle Eastern	0.000109	0.000109
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Alpha-2,6-sialyltransferase involved in the synthesis of alpha-series gangliosides. Has activity toward GD1a, GT1b and GM1b. Has no activity toward glycoproteins. Responsible for the biosynthesis of DSGG (disialylgalactosylgloboside) from MSGG (monosialylgalactosylgloboside) in normal and malignant kidney. Participates in the synthesis of disialyl Lewis a (Le(a)). {ECO:0000269|PubMed:12668675, ECO:0000269|PubMed:17123352}.
• Pathway: Glycosphingolipid biosynthesis - ganglio series - Homo sapiens (human);Ganglio Sphingolipid Metabolism;Globo Sphingolipid Metabolism;Post-translational protein modification;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;Asparagine N-linked glycosylation (Consensus)

Recessive Scores

• pRec: 0.0931

Intolerance Scores

• rvis_EVS: -1.02
• rvis_percentile_EVS: 7.94

Haploinsufficiency Scores

• pHI: 0.140
• hipred: N
• hipred_score: 0.417
• ghis: 0.578

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.365

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: St6galnac6

Gene ontology

• Biological process: ganglioside biosynthetic process;protein glycosylation;glycosylceramide metabolic process;glycosphingolipid metabolic process;glycoprotein metabolic process;oligosaccharide biosynthetic process;cell-cell recognition;sialylation
• Cellular component: Golgi membrane;cytoplasm;plasma membrane;integral component of membrane
• Molecular function: alpha-N-acetylgalactosaminide alpha-2,6-sialyltransferase activity;sialyltransferase activity