ST3GAL4

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

Basic information

Region (hg38): 11:126355639-126440344

Previous symbols: [ "CGS23", "SIAT4", "NANTA3", "SIAT4C" ]

Links

ENSG00000110080 ∙ NCBI:6484 ∙ OMIM:104240 ∙ HGNC:10864 ∙ Uniprot:Q11206 ∙ 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 ST3GAL4 gene.

• Inborn genetic diseases (8 variants)
• not specified (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ST3GAL4 gene is commonly pathogenic or not.

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.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous					2	2
missense			8			8
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	8	0	2

Variants in ST3GAL4

This is a list of pathogenic ClinVar variants found in the ST3GAL4 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
11-126406499-C-G		not specified	Uncertain significance (Apr 13, 2022)
11-126406536-G-A		not specified	Uncertain significance (Sep 01, 2021)
11-126406951-T-C		not specified	Uncertain significance (Feb 15, 2023)
11-126406962-G-A		not specified	Uncertain significance (Mar 01, 2024)
11-126406975-C-T		not specified	Uncertain significance (Jul 13, 2022)
11-126407260-G-A		not specified	Uncertain significance (May 31, 2023)
11-126407304-A-G		not specified	Uncertain significance (Oct 10, 2023)
11-126407308-C-T		not specified	Uncertain significance (Aug 08, 2023)
11-126407321-C-T		not specified	Benign (-)
11-126408112-C-T		not specified	Uncertain significance (Apr 12, 2023)
11-126408146-G-A		not specified	Uncertain significance (Nov 17, 2022)
11-126408180-C-T		not specified	Benign (-)
11-126408308-T-C		not specified	Benign (-)
11-126408467-A-G		not specified	Uncertain significance (Dec 14, 2023)
11-126409314-A-G		not specified	Uncertain significance (Jan 04, 2024)
11-126424569-G-A			Benign (Jan 22, 2019)
11-126424615-G-A		Developmental disorder	Likely benign (Oct 21, 2021)
11-126424637-C-T			Likely benign (Jul 29, 2018)
11-126424688-G-A		not specified	Likely benign (Oct 23, 2019)
11-126424715-G-A		KIRREL3-related disorder	Likely benign (Dec 16, 2019)
11-126424726-C-A		Intellectual disability, autosomal dominant 4	Uncertain significance (Jul 25, 2018)
11-126424726-C-T			Uncertain significance (Nov 19, 2015)
11-126424743-G-A		not specified	Uncertain significance (Sep 20, 2023)
11-126424766-G-A		not specified	Benign (Dec 31, 2019)
11-126424799-A-C		KIRREL3-related disorder	Benign/Likely benign (Feb 07, 2020)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ST3GAL4	protein_coding	protein_coding	ENST00000526727	10	84705

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0398	0.959	125740	0	8	125748	0.0000318

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.58	143	207	0.691	0.0000129	2184
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000615	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000440	0.0000439
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.000163	0.000163

dbNSFP

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}.
• Pathway: Glycosphingolipid biosynthesis - lacto and neolacto series - Homo sapiens (human);Signal Transduction;Metabolism of carbohydrates;Keratan sulfate biosynthesis;Keratan sulfate/keratin metabolism;Glycosaminoglycan metabolism;Post-translational protein modification;N-Glycan antennae elongation;N-glycan antennae elongation in the medial/trans-Golgi;Metabolism of proteins;Glycosphingolipid biosynthesis - ganglioseries;Glycosphingolipid biosynthesis - globoseries;Metabolism;mucin core 1 and core 2 <i>O</i>-glycosylation;Pre-NOTCH Processing in Golgi;Pre-NOTCH Expression and Processing;Signaling by NOTCH;O-Glycan biosynthesis;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;Transport to the Golgi and subsequent modification;Asparagine N-linked glycosylation;Termination of O-glycan biosynthesis;O-linked glycosylation of mucins;O-linked glycosylation (Consensus)

Recessive Scores

• pRec: 0.145

Intolerance Scores

• loftool: 0.422
• rvis_EVS: 0.04
• rvis_percentile_EVS: 56.92

Haploinsufficiency Scores

• pHI: 0.0702
• hipred: Y
• hipred_score: 0.728
• ghis: 0.434

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.150

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: St3gal4
• Phenotype: hematopoietic system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); immune system phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); homeostasis/metabolism phenotype; cellular phenotype

Gene ontology

• Biological process: protein glycosylation;glycoprotein biosynthetic process;glycolipid biosynthetic process;oligosaccharide biosynthetic process;O-glycan processing;keratan sulfate biosynthetic process;lipid glycosylation;cognition;sialylation;protein sialylation
• Cellular component: Golgi membrane;extracellular region;membrane;integral component of membrane;Golgi cisterna membrane
• Molecular function: beta-galactoside (CMP) alpha-2,3-sialyltransferase activity;sialyltransferase activity;monosialoganglioside sialyltransferase activity