ST8SIA2

protein-coding

ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 2, the group of Sialyltransferases

Gene summary

The protein encoded by this gene is a type II membrane protein that is thought to catalyze the transfer of sialic acid from CMP-sialic acid to N-linked oligosaccharides and glycoproteins. The encoded protein may be found in the Golgi apparatus and may be involved in the production of polysialic acid, a modulator of the adhesive properties of neural cell adhesion molecule (NCAM1). This protein is a member of glycosyltransferase family 29. [provided by RefSeq, Jul 2008]

Previous symbols:

SIAT8B

MANE transcript

NM_006011.4

Inheritance

ClinVar variants

U:40B:6

Top phenotype

ST8SIA2-related disorder

gnomAD constraint

pLI —, LoF o/e 0.31

Max pathogenic AF

—

Genomic locus

chr15:92,393,881-92,468,728

External References & Databases

Ensembl (ENSG00000140557)

Transcript & Mutation Effects

hg38 • Region Span ~74.8 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

schizophreniaLIMITED

Inheritance Pattern: AD

Disease ID:MONDO:0005090

Submitter: Ambry Genetics

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to ST8SIA2 variants in ClinVar

4 Conditions Cataloged

not specifiedTotal: 40

not providedTotal: 4

ST8SIA2-related disorderTotal: 4

EBV-positive nodal T- and NK-cell lymphomaTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_006011.4. 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				3 clinvar	1 clinvar	4
missense			40 clinvar	1 clinvar		41
nonsense				1 clinvar		1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	40	5	1	46

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 9 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_006011.4	RefSeq	NP_006002.1	6	MANE Select
ENST00000268164.8	Ensembl	ENSP00000268164.3	6	MANE Select
NM_001330416.2	RefSeq	NP_001317345.1	5	Standard
ENST00000539113.5	Ensembl	ENSP00000437382.1	5	Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / Model	Organism	Observed Phenotype
st8sia2	Danio rerio	Structure: diencephalic white matter Quality: decreased amount abnormal

Gene / Model

Organism

Observed Phenotype

st8sia2

Danio rerio

Structure: diencephalic white matter

Quality: decreased amount

abnormal

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Developmental Biology
Post-translational protein modification
N-Glycan antennae elongation
N-glycan antennae elongation in the medial/trans-Golgi
Metabolism of proteins

Biological Process

ganglioside biosynthetic process
carbohydrate metabolic process
cellular protein modification process
protein glycosylation
N-glycan processing

Molecular Function

alpha-N-acetylneuraminate alpha-2,8-sialyltransferase activity
sialic acid binding

Cellular Component

Golgi membrane
early endosome
integral component of membrane
recycling endosome

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000268164
Coding exons: 6
Length: 74901
Individuals with no LoFs: 125744
Homozygous LoFs: 0
Heterozygous LoFs: 4
Defined: 125748
p: 0.0000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.50	160	223	0.717	0.0000140	2437
Missense (PolyPhen)		35	84.637	0.41353		913
Synonymous	-1.28	114	97.9	1.16	0.00000672	741
Loss of Function	2.57	5	16.2	0.309	7.63e-7	188

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.000026	0.000026	rare
South Asian	0	0.0	absent
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May transfer sialic acid through alpha-2,8-linkages to the alpha-2,3-linked and alpha-2,6-linked sialic acid of N-linked oligosaccharides of glycoproteins and may be involved in PSA (polysialic acid) expression.;

Recessive Scores

pRec: 0.268

Intolerance Scores

LoFtool: 0.155
RVIS EVS: -0.42
RVIS percentile EVS: 25.56

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.802

Gene Damage Prediction

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