ST3GAL3

ST3 beta-galactoside alpha-2,3-sialyltransferase 3, the group of Sialyltransferases|MicroRNA protein coding host genes

Basic information

Region (hg38): 1:43705824-43931165

Previous symbols: [ "SIAT6", "MRT12" ]

Links

ENSG00000126091

∙ NCBI:6487 ∙ OMIM:606494 ∙ HGNC:10866 ∙ Uniprot:Q11203 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

intellectual disability, autosomal recessive 12 (Strong), mode of inheritance: AR
developmental and epileptic encephalopathy, 15 (Limited), mode of inheritance: AR
infantile spasms (Supportive), mode of inheritance: AD
autosomal recessive non-syndromic intellectual disability (Supportive), mode of inheritance: AR
developmental and epileptic encephalopathy, 15 (Strong), mode of inheritance: AR
complex neurodevelopmental disorder (Moderate), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Intellectual development disorder, autosomal recessive 12; Developmental and epileptic encephalopathy 15	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Neurologic	17120046; 21907012; 23252400
As with other conditions involving seizures, optimal seizure control is beneficial, and awareness of genetic causes may help with medication selection

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ST3GAL3 gene.

Developmental_and_epileptic_encephalopathy (301 variants)
Inborn_genetic_diseases (72 variants)
not_provided (58 variants)
not_specified (23 variants)
Developmental_and_epileptic_encephalopathy,_15 (20 variants)
Intellectual_disability,_autosomal_recessive_12 (15 variants)
ST3GAL3-related_disorder (10 variants)
Intellectual_disability (3 variants)
Epilepsy_due_to_perinatal_stroke (1 variants)
Aggressive_behavior (1 variants)
Generalized_myoclonic_seizure (1 variants)
Prolonged_neonatal_jaundice (1 variants)
Difficulty_walking (1 variants)
Intellectual_disability,_severe (1 variants)
Frequent_falls (1 variants)
Developmental_and_epileptic_encephalopathy,_1 (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ST3GAL3 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000006279.5. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous			5 clinvar	91 clinvar		96
missense	3 clinvar	1 clinvar	129 clinvar	1 clinvar		134
nonsense	4 clinvar	2 clinvar				6
start loss			1			1
frameshift	2 clinvar	1 clinvar	2 clinvar			5
splice donor/acceptor (+/-2bp)	2 clinvar	9 clinvar				11
Total	11	13	137	92	0

Highest pathogenic variant AF is 0.000028045886

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ST3GAL3	protein_coding	protein_coding	ENST00000262915	12	225337

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00256	0.997	125719	0	29	125748	0.000115

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.50	188	255	0.736	0.0000172	2854
Missense in Polyphen		49	92.206	0.53142		1059
Synonymous	0.275	101	105	0.966	0.00000735	904
Loss of Function	3.00	9	25.3	0.356	0.00000144	301

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000867	0.0000867
Ashkenazi Jewish	0.000198	0.000198
East Asian	0.000272	0.000272
Finnish	0.00	0.00
European (Non-Finnish)	0.0000615	0.0000615
Middle Eastern	0.000272	0.000272
South Asian	0.000392	0.000392
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Function: FUNCTION: Catalyzes the formation of the NeuAc-alpha-2,3-Gal-beta- 1,4-GlcNAc-, NeuAc-alpha-2,3-Gal-beta-1,3-GlcNAc- and NeuAc-alpha- 2,3-Gal-beta-1,3-GalNAc- sequences found in terminal carbohydrate groups of glycoproteins and glycolipids. The highest activity is toward Gal-beta-1,3-GlcNAc and the lowest toward Gal-beta-1,3- GalNAc. {ECO:0000250|UniProtKB:P97325}.;
Disease: DISEASE: Mental retardation, autosomal recessive 12 (MRT12) [MIM:611090]: A disorder characterized by significantly below average general intellectual functioning associated with impairments in adaptive behavior and manifested during the developmental period. {ECO:0000269|PubMed:21907012}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Epileptic encephalopathy, early infantile, 15 (EIEE15) [MIM:615006]: A form of epilepsy that manifests in the neonatal or the early infantile period as severely impaired cognitive and motor development, due to recurrent clinical seizures or prominent interictal epileptiform discharges. Patients develop infantile spasms, mainly of the flexor type, between 3 and 7 months of age, which are accompanied by hypsarrhythmia on EEG. Other features include poor eye contact, hypotonia, primitive reflexes, and irritability. Seizures evolve clinically to Lennox-Gastaut syndrome. {ECO:0000269|PubMed:23252400}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
Pathway: Other types of O-glycan biosynthesis - Homo sapiens (human);Mannose type O-glycan biosynthesis - Homo sapiens (human);Glycosphingolipid biosynthesis - lacto and neolacto series - Homo sapiens (human);Glycosaminoglycan biosynthesis - keratan sulfate - Homo sapiens (human);Glycosphingolipid biosynthesis - lactoseries;Signal Transduction;Metabolism of carbohydrates;Keratan sulfate biosynthesis;Keratan sulfate/keratin metabolism;Glycosaminoglycan metabolism;Post-translational protein modification;Metabolism of proteins;Metabolism;Pre-NOTCH Processing in Golgi;Pre-NOTCH Expression and Processing;Signaling by NOTCH;terminal <i>O</i>-glycans residues modification;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;Asparagine N-linked glycosylation;Termination of O-glycan biosynthesis;O-linked glycosylation of mucins;O-linked glycosylation (Consensus)

Recessive Scores

pRec: 0.106

Intolerance Scores

loftool: 0.589
rvis_EVS: -0.36
rvis_percentile_EVS: 29.16

Haploinsufficiency Scores

pHI: 0.351
hipred: Y
hipred_score: 0.625
ghis: 0.667

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.871

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: St3gal3
Phenotype

Gene ontology

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