GeneBe

ST6GALNAC2

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

Basic information

Region (hg38): 17:76565377-76586956

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.

  • not_specified (62 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. These statistics are base on transcript: NM_000006456.3. Only rare variants are included in the table.

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.

EffectPLPVUSLBBSum
synonymous
0
missense
60
clinvar
2
clinvar
 62
nonsense
0
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
0
Total 0 0 60 2 0
Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
ST6GALNAC2protein_codingprotein_codingENST00000225276 923247
pLI Probability
LOF Intolerant 		pRec Probability
LOF Recessive 		Individuals with
no LOFs 		Individuals with
Homozygous LOFs 		Individuals with
Heterozygous LOFs 		Defined p
7.47e-150.004621256591881257480.000354
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.2422052150.9540.00001272400
Missense in Polyphen7990.7160.87085988
Synonymous-0.88110796.01.110.00000606768
Loss of Function-0.6402017.11.178.10e-7199

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0009330.000931
Ashkenazi Jewish0.0001010.0000992
East Asian0.00005440.0000544
Finnish0.000.00
European (Non-Finnish)0.0005530.000501
Middle Eastern0.00005440.0000544
South Asian0.0001960.000163
Other0.0003320.000326

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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