ST6GALNAC4

ST6 N-acetylgalactosaminide alpha-2,6-sialyltransferase 4, the group of Sialyltransferases

Basic information

Region (hg38): 9:127907886-127917041

Previous symbols: [ "SIAT7D" ]

Links

ENSG00000136840 ∙ NCBI:27090 ∙ OMIM:606378 ∙ HGNC:17846 ∙ Uniprot:Q9H4F1 ∙ 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 ST6GALNAC4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ST6GALNAC4 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					2	2
missense			30	1		31
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	30	1	2

Variants in ST6GALNAC4

This is a list of pathogenic ClinVar variants found in the ST6GALNAC4 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-127908402-C-T		not specified	Uncertain significance (Jun 17, 2024)
9-127908447-C-T		not specified	Uncertain significance (Sep 20, 2024)
9-127908477-C-T		not specified	Uncertain significance (May 09, 2022)
9-127910002-T-C		not specified	Uncertain significance (Dec 06, 2022)
9-127910018-T-C		not specified	Uncertain significance (Nov 07, 2022)
9-127910050-G-A		not specified	Uncertain significance (Nov 18, 2023)
9-127912269-G-A		not specified	Uncertain significance (Jan 09, 2025)
9-127912302-C-T		not specified	Uncertain significance (Apr 03, 2023)
9-127912362-T-C		not specified	Uncertain significance (May 20, 2024)
9-127912379-C-T		not specified	Uncertain significance (Jun 21, 2021)
9-127912380-G-A		not specified	Uncertain significance (Nov 13, 2024)
9-127912382-T-C		not specified	Uncertain significance (Apr 18, 2023)
9-127912394-C-T		not specified	Uncertain significance (Jan 03, 2025)
9-127912403-C-T		not specified	Uncertain significance (May 15, 2024)
9-127912411-G-A			Benign (Nov 28, 2018)
9-127912414-C-A		not specified	Uncertain significance (Dec 18, 2023)
9-127912479-G-A		not specified	Uncertain significance (Jan 04, 2024)
9-127912490-G-A		not specified	Uncertain significance (Mar 28, 2022)
9-127912494-C-G		not specified	Uncertain significance (Jan 18, 2023)
9-127912527-G-A		not specified	Uncertain significance (May 29, 2024)
9-127912541-G-C		not specified	Uncertain significance (Nov 21, 2023)
9-127912545-C-T		not specified	Uncertain significance (Oct 10, 2023)
9-127912562-G-C		not specified	Uncertain significance (Nov 14, 2024)
9-127912581-C-T		not specified	Uncertain significance (Jul 20, 2021)
9-127912638-T-C		not specified	Uncertain significance (Oct 02, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ST6GALNAC4	protein_coding	protein_coding	ENST00000335791	5	9153

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.52e-7	0.353	125651	2	86	125739	0.000350

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.764	174	205	0.850	0.0000142	1941
Missense in Polyphen		74	92.428	0.80062		846
Synonymous	0.408	86	90.9	0.946	0.00000683	607
Loss of Function	0.540	11	13.1	0.839	7.29e-7	138

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000565	0.000562
Ashkenazi Jewish	0.00	0.00
East Asian	0.000163	0.000163
Finnish	0.00236	0.00231
European (Non-Finnish)	0.000156	0.000132
Middle Eastern	0.000163	0.000163
South Asian	0.0000983	0.0000980
Other	0.000165	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in the biosynthesis of ganglioside GD1A from GM1B. Transfers CMP-NeuAc with an alpha-2,6-linkage to GalNAc residue on NeuAc-alpha-2,3-Gal-beta-1,3-GalNAc of glycoproteins and glycolipids. Prefers glycoproteins to glycolipids (By similarity). {ECO:0000250}.
• Pathway: Glycosphingolipid biosynthesis - ganglio series - Homo sapiens (human);Globo Sphingolipid Metabolism;Post-translational protein modification;Metabolism of proteins;Glycosphingolipid biosynthesis - ganglioseries;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;Termination of O-glycan biosynthesis;O-linked glycosylation of mucins;O-linked glycosylation (Consensus)

Recessive Scores

• pRec: 0.114

Intolerance Scores

• loftool: 0.556
• rvis_EVS: -0.58
• rvis_percentile_EVS: 18.59

Haploinsufficiency Scores

• pHI: 0.151
• hipred: N
• hipred_score: 0.170
• ghis: 0.562

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.156

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: St6galnac4

Gene ontology

• Biological process: glycolipid metabolic process;O-glycan processing;sialylation
• Cellular component: Golgi membrane;integral component of membrane
• Molecular function: alpha-N-acetylgalactosaminide alpha-2,6-sialyltransferase activity;sialyltransferase activity;(alpha-N-acetylneuraminyl-2,3-beta-galactosyl-1,3)-N-acetyl-galactosaminide 6-alpha-sialyltransferase activity