ST6GALNAC5

ST6 N-acetylgalactosaminide alpha-2,6-sialyltransferase 5, the group of Sialyltransferases|MicroRNA protein coding host genes

Basic information

Region (hg38): 1:76867480-77067546

Previous symbols: [ "SIAT7E" ]

Links

ENSG00000117069 ∙ NCBI:81849 ∙ OMIM:610134 ∙ HGNC:19342 ∙ Uniprot:Q9BVH7 ∙ 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 ST6GALNAC5 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ST6GALNAC5 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					1	1
missense			26			26
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	26	0	1

Variants in ST6GALNAC5

This is a list of pathogenic ClinVar variants found in the ST6GALNAC5 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-76868492-C-T			Benign (Apr 04, 2018)
1-76868501-A-G		not specified	Uncertain significance (Mar 07, 2024)
1-76868554-G-A		not specified	Uncertain significance (Sep 26, 2023)
1-76868635-G-A		not specified	Uncertain significance (Sep 26, 2023)
1-76868647-T-C		not specified	Uncertain significance (Nov 07, 2022)
1-76868683-C-T		not specified	Uncertain significance (May 30, 2024)
1-76868705-G-T		not specified	Uncertain significance (Nov 28, 2023)
1-77044267-C-T		not specified	Uncertain significance (Mar 23, 2023)
1-77044288-C-A		not specified	Uncertain significance (Nov 08, 2022)
1-77044306-C-T		not specified	Uncertain significance (Feb 27, 2024)
1-77044318-G-A		not specified	Uncertain significance (Nov 08, 2021)
1-77044323-C-T			Benign (Dec 31, 2019)
1-77044330-G-A		not specified	Uncertain significance (Dec 18, 2023)
1-77044402-C-T		not specified	Uncertain significance (Mar 13, 2023)
1-77044403-G-A		not specified	Uncertain significance (Feb 27, 2023)
1-77044405-A-T		not specified	Uncertain significance (Jun 17, 2024)
1-77044434-G-C		not specified	Uncertain significance (Oct 10, 2023)
1-77044483-G-A		not specified	Uncertain significance (Feb 27, 2023)
1-77044499-A-G		not specified	Uncertain significance (Jun 06, 2023)
1-77044506-C-G		not specified	Uncertain significance (May 31, 2023)
1-77044513-C-T		not specified	Uncertain significance (Nov 07, 2023)
1-77044525-G-C		not specified	Uncertain significance (Apr 05, 2023)
1-77044549-A-G		not specified	Uncertain significance (Mar 27, 2023)
1-77044571-T-A		not specified	Uncertain significance (Nov 06, 2023)
1-77050323-A-G		not specified	Uncertain significance (Feb 03, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ST6GALNAC5	protein_coding	protein_coding	ENST00000477717	5	198271

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.170	0.828	125727	0	21	125748	0.0000835

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.541	185	207	0.894	0.0000120	2215
Missense in Polyphen		73	100.47	0.72662		1066
Synonymous	-0.554	85	78.7	1.08	0.00000420	649
Loss of Function	2.62	4	15.0	0.268	8.23e-7	151

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000291	0.000268
Ashkenazi Jewish	0.000103	0.0000992
East Asian	0.000163	0.000163
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000559	0.0000439
Middle Eastern	0.000163	0.000163
South Asian	0.000164	0.000131
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in the biosynthesis of ganglioside GD1a from GM1b. It exhibits higher activity with glycolipids than with glycoproteins (By similarity). {ECO:0000250}.
• Pathway: Glycosphingolipid biosynthesis - ganglio series - Homo sapiens (human);Globo Sphingolipid Metabolism;Post-translational protein modification;Metabolism of proteins;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 (Consensus)

Recessive Scores

• pRec: 0.113

Intolerance Scores

• loftool: 0.306
• rvis_EVS: -0.47
• rvis_percentile_EVS: 23.04

Haploinsufficiency Scores

• pHI: 0.522
• hipred: Y
• hipred_score: 0.745
• ghis: 0.603

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.262

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: St6galnac5

Gene ontology

• Biological process: protein glycosylation;glycosphingolipid biosynthetic process;oligosaccharide biosynthetic process;sialylation
• Cellular component: Golgi membrane;integral component of membrane
• Molecular function: alpha-N-acetylgalactosaminide alpha-2,6-sialyltransferase activity;sialyltransferase activity