ST3GAL1

protein-coding

ST3 beta-galactoside alpha-2,3-sialyltransferase 1, the group of Sialyltransferases

Gene summary

The protein encoded by this gene is a type II membrane protein that catalyzes the transfer of sialic acid from CMP-sialic acid to galactose-containing substrates. The encoded protein is normally found in the Golgi but can be proteolytically processed to a soluble form. Correct glycosylation of the encoded protein may be critical to its sialyltransferase activity. This protein, which is a member of glycosyltransferase family 29, can use the same acceptor substrates as does sialyltransferase 4B. Two transcript variants encoding the same protein have been found for this gene. Other transcript variants may exist, but have not been fully characterized yet. [provided by RefSeq, Jul 2008]

Previous symbols:

SIAT4A

MANE transcript

NM_173344.3

Inheritance

—

ClinVar variants

U:44B:5

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.19

Max pathogenic AF

—

Genomic locus

chr8:133,454,848-133,571,926

External References & Databases

Ensembl (ENSG00000008513)

Transcript & Mutation Effects

hg38 • Region Span ~117.1 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 ST3GAL1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 39

not providedTotal: 4

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_173344.3. 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		2 clinvar	4
missense			39 clinvar	2 clinvar	1 clinvar	42
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			3 clinvar			3
Total	0	0	44	2	3	49

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 185 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_173344.3	RefSeq	NP_775479.1	6	MANE Select
ENST00000522652.6	Ensembl	ENSP00000430515.1	6	MANE Select
NM_003033.4	RefSeq	NP_003024.1	6	Standard
ENST00000517668.5	Ensembl	ENSP00000427720.1	2	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Glycosphingolipid biosynthesis - ganglio series - Homo sapiens (human)
Mucin type O-glycan biosynthesis - Homo sapiens (human)
Glycosphingolipid biosynthesis - globo and isoglobo series - Homo sapiens (human)
Glycosaminoglycan biosynthesis - keratan sulfate - Homo sapiens (human)
Ganglio Sphingolipid Metabolism

Biological Process

N-acetylneuraminate metabolic process
cellular protein modification process
protein phosphorylation
protein N-linked glycosylation
O-glycan processing

Molecular Function

beta-galactoside (CMP) alpha-2,3-sialyltransferase activity

Cellular Component

Golgi membrane
membrane
integral component of membrane
Golgi cisterna membrane
extracellular exosome

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000319914
Coding exons: 6
Length: 117093
Individuals with no LoFs: 125735
Homozygous LoFs: 0
Heterozygous LoFs: 7
Defined: 125742
p: 0.0000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.30	161	215	0.751	0.0000132	2244
Missense (PolyPhen)		63	91.966	0.68503		955
Synonymous	0.313	90	93.9	0.959	0.00000651	662
Loss of Function	2.97	3	15.7	0.191	8.28e-7	161

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00012	0.00012	rare
Latino/Admixed American	0.000029	0.000029	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.000035	0.000035	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Responsible for the synthesis of the sequence NeuAc- alpha-2,3-Gal-beta-1,3-GalNAc- found on sugar chains O-linked to Thr or Ser and also as a terminal sequence on certain gangliosides. SIAT4A and SIAT4B sialylate the same acceptor substrates but exhibit different Km values. {ECO:0000250|UniProtKB:P54751}.;

Recessive Scores

pRec: 0.144

Intolerance Scores

LoFtool: 0.351
RVIS EVS: 0.29
RVIS percentile EVS: 71.5

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Indispensability pred.: N
Indispensability score: 0.242

Gene Damage Prediction

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