ST6GALNAC2

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

Basic information

Region (hg38): 17:76565376-76586956

Previous symbols: [ "SIAT7", "SIAT7B", "SIATL1" ]

Links

ENSG00000070731 ∙ NCBI:10610 ∙ OMIM:610137 ∙ HGNC:10867 ∙ Uniprot:Q9UJ37 ∙ 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 ST6GALNAC2 gene.

• Inborn genetic diseases (21 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ST6GALNAC2 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			21			21
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	21	0	0

Variants in ST6GALNAC2

This is a list of pathogenic ClinVar variants found in the ST6GALNAC2 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-76566115-A-G		not specified	Uncertain significance (Oct 26, 2022)
17-76566175-C-T		not specified	Uncertain significance (Mar 27, 2023)
17-76566226-C-T		not specified	Uncertain significance (Jul 12, 2023)
17-76566245-G-C		not specified	Uncertain significance (Dec 14, 2022)
17-76567505-A-G		not specified	Uncertain significance (Dec 21, 2023)
17-76570592-A-G		not specified	Uncertain significance (Nov 07, 2022)
17-76572644-T-C		not specified	Uncertain significance (Apr 26, 2023)
17-76572731-G-A		not specified	Uncertain significance (Oct 06, 2022)
17-76572747-C-T		not specified	Uncertain significance (Jun 02, 2023)
17-76573217-C-T		not specified	Uncertain significance (Mar 07, 2024)
17-76573249-A-T		not specified	Uncertain significance (Jan 03, 2024)
17-76573256-C-T		not specified	Uncertain significance (Jun 29, 2022)
17-76573276-C-T		not specified	Uncertain significance (Dec 17, 2023)
17-76573325-T-A		not specified	Uncertain significance (Oct 22, 2021)
17-76574367-T-C		not specified	Uncertain significance (Oct 10, 2023)
17-76574370-T-A		not specified	Uncertain significance (Oct 12, 2021)
17-76574383-G-C		not specified	Uncertain significance (Dec 01, 2022)
17-76574398-C-T		not specified	Uncertain significance (Feb 26, 2024)
17-76574401-T-G		not specified	Uncertain significance (Dec 14, 2021)
17-76574409-C-T		not specified	Uncertain significance (Dec 05, 2022)
17-76574416-G-A		not specified	Uncertain significance (Sep 16, 2021)
17-76574442-T-A		not specified	Uncertain significance (Dec 13, 2023)
17-76574448-C-A		not specified	Uncertain significance (Jul 11, 2023)
17-76574472-T-C		not specified	Uncertain significance (Nov 07, 2023)
17-76574476-A-G		not specified	Uncertain significance (Aug 03, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ST6GALNAC2	protein_coding	protein_coding	ENST00000225276	9	23247

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
7.47e-15	0.00462	125659	1	88	125748	0.000354

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.242	205	215	0.954	0.0000127	2400
Missense in Polyphen		79	90.716	0.87085		988
Synonymous	-0.881	107	96.0	1.11	0.00000606	768
Loss of Function	-0.640	20	17.1	1.17	8.10e-7	199

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000933	0.000931
Ashkenazi Jewish	0.000101	0.0000992
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.000553	0.000501
Middle Eastern	0.0000544	0.0000544
South Asian	0.000196	0.000163
Other	0.000332	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Catalyzes the transfer of N-acetylneuraminyl groups onto glycan chains in glycoproteins. {ECO:0000269|PubMed:10742600, ECO:0000269|PubMed:29251719}.
• Pathway: 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;Termination of O-glycan biosynthesis;O-linked glycosylation of mucins;O-linked glycosylation (Consensus)

Recessive Scores

• pRec: 0.128

Intolerance Scores

• loftool: 0.759
• rvis_EVS: 0.0000761
• rvis_percentile_EVS: 53.98

Haploinsufficiency Scores

• pHI: 0.0696
• hipred: N
• hipred_score: 0.219
• ghis: 0.443

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.483

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: St6galnac2
• Phenotype: homeostasis/metabolism phenotype; growth/size/body region phenotype; hematopoietic system phenotype; immune system phenotype

Gene ontology

• Biological process: protein glycosylation;protein O-linked glycosylation;O-glycan processing;protein sialylation
• Cellular component: Golgi membrane;integral component of membrane
• Molecular function: alpha-N-acetylgalactosaminide alpha-2,6-sialyltransferase activity;sialyltransferase activity