ST3GAL4

protein-coding

ST3 beta-galactoside alpha-2,3-sialyltransferase 4, the group of Sialyltransferases

Gene summary

This gene encodes a member of the glycosyltransferase 29 family, a group of enzymes involved in protein glycosylation. The encoded protein is targeted to Golgi membranes but may be proteolytically processed and secreted. The gene product may also be involved in the increased expression of sialyl Lewis X antigen seen in inflammatory responses. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2011]

Previous symbols:

CGS23
SIAT4
NANTA3
SIAT4C

MANE transcript

NM_001254757.2

Inheritance

—

ClinVar variants

U:48B:3

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.31

Max pathogenic AF

—

Genomic locus

chr11:126,355,640-126,440,344

External References & Databases

Ensembl (ENSG00000110080)

Transcript & Mutation Effects

hg38 • Region Span ~84.7 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 ST3GAL4 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 43

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001254757.2. 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			1 clinvar			1
missense			42 clinvar	3 clinvar		45
nonsense			2 clinvar			2
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			3 clinvar			3
Total	0	0	48	3	0	51

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 140 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001254757.2	RefSeq	NP_001241686.1	10	MANE Select
ENST00000444328.7	Ensembl	ENSP00000394354.2	10	MANE Select
NM_001254758.2	RefSeq	NP_001241687.1	10	Standard
NM_001254759.2	RefSeq	NP_001241688.1	9	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Glycosphingolipid biosynthesis - lacto and neolacto series - Homo sapiens (human)
Signal Transduction
Metabolism of carbohydrates
Keratan sulfate biosynthesis
Keratan sulfate/keratin metabolism

Biological Process

protein glycosylation
glycoprotein biosynthetic process
glycolipid biosynthetic process
oligosaccharide biosynthetic process
O-glycan processing

Molecular Function

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

Cellular Component

Golgi membrane
extracellular region
membrane
integral component of membrane
Golgi cisterna membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000526727
Coding exons: 10
Length: 84705
Individuals with no LoFs: 125740
Homozygous LoFs: 0
Heterozygous LoFs: 8
Defined: 125748
p: 0.0000318

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.58	143	207	0.691	0.0000129	2184
Missense (PolyPhen)		41	76.924	0.53299		766
Synonymous	0.861	70	79.8	0.877	0.00000473	646
Loss of Function	2.83	6	19.5	0.308	0.00000101	213

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000062	0.000062	rare
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.000044	0.000044	rare
South Asian	0	0.0	absent
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Catalyzes the formation of the NeuAc-alpha-2,3-Gal-beta- 1,4-GlcNAc-, and NeuAc-alpha-2,3-Gal-beta-1,3-GlcNAc- sequences found in terminal carbohydrate groups of glycoproteins and glycolipids. It may be involved in the biosynthesis of the sialyl Lewis X determinant. {ECO:0000250|UniProtKB:Q91Y74, ECO:0000269|PubMed:8611500}.;

Recessive Scores

pRec: 0.145

Intolerance Scores

LoFtool: 0.422
RVIS EVS: 0.04
RVIS percentile EVS: 56.92

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.150

Gene Damage Prediction

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