ST6GAL2

protein-coding

ST6 beta-galactoside alpha-2,6-sialyltransferase 2, the group of Sialyltransferases

Gene summary

This locus encodes a sialyltransferase. The encoded type II transmembrane protein catalyzes the transfer of sialic acid from CMP to an oligosaccharide substrate. Polymorphisms at this locus may be associated with variations in risperidone response in schizophrenic patients. Alternatively spliced transcript variants have been described. [provided by RefSeq, Jan 2012]

Previous symbols:

SIAT2

MANE transcript

NM_001142351.2

Inheritance

—

ClinVar variants

U:67B:6

Top phenotype

EBV-positive nodal T- and NK-cell lymphoma

gnomAD constraint

pLI —, LoF o/e 0.38

Max pathogenic AF

—

Genomic locus

chr2:106,801,600-106,887,108

External References & Databases

Ensembl (ENSG00000144057)

Transcript & Mutation Effects

hg38 • Region Span ~85.5 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to ST6GAL2 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 67

EBV-positive nodal T- and NK-cell lymphomaTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001142351.2. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			2 clinvar	1 clinvar		3
missense			65 clinvar	5 clinvar		70
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	67	6	0	73

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 34 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001142351.2	RefSeq	NP_001135823.1	5	MANE Select
ENST00000409382.8	Ensembl	ENSP00000386942.3	5	MANE Select
NM_001142352.2	RefSeq	NP_001135824.1	5	Standard
NM_001322362.2	RefSeq	NP_001309291.1	5	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

N-Glycan biosynthesis - Homo sapiens (human)
Other types of O-glycan biosynthesis - Homo sapiens (human)
Globo Sphingolipid Metabolism
Post-translational protein modification
Metabolism of proteins

Biological Process

protein glycosylation
oligosaccharide metabolic process
sialylation

Molecular Function

beta-galactoside alpha-2,6-sialyltransferase activity

Cellular Component

Golgi membrane
integral component of membrane
Golgi cisterna membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000409382
Coding exons: 5
Length: 85509
Individuals with no LoFs: 125723
Homozygous LoFs: 0
Heterozygous LoFs: 25
Defined: 125748
p: 0.0000994

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.211	324	335	0.968	0.0000221	3427
Missense (PolyPhen)		106	133.58	0.7935		1409
Synonymous	0.326	141	146	0.966	0.0000107	1072
Loss of Function	2.49	7	18.6	0.376	8.94e-7	205

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000088	0.000087	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000054	0.000054	rare
Finnish	0.00014	0.00014	rare
European (Non-Finnish)	0.00012	0.00011	rare
South Asian	0.00013	0.00013	rare
Other	0.00017	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Transfers sialic acid from the donor of substrate CMP- sialic acid to galactose containing acceptor substrates. Has alpha-2,6-sialyltransferase activity toward oligosaccharides that have the Gal-beta-1,4-GlcNAc sequence at the non-reducing end of their carbohydrate groups, but it has weak or no activities toward glycoproteins and glycolipids. {ECO:0000269|PubMed:12235148}.;

Recessive Scores

pRec: 0.112

Intolerance Scores

LoFtool: 0.795
RVIS EVS: 1.73
RVIS percentile EVS: 96.6

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.136

Gene Damage Prediction

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