ST6GALNAC1

ST6 N-acetylgalactosaminide alpha-2,6-sialyltransferase 1, the group of Sialyltransferases

Basic information

Region (hg38): 17:76624761-76643786

Previous symbols: [ "SIAT7A" ]

Links

ENSG00000070526 ∙ NCBI:55808 ∙ OMIM:610138 ∙ HGNC:23614 ∙ Uniprot:Q9NSC7 ∙ 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 ST6GALNAC1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ST6GALNAC1 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						0
missense			32	3	1	36
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	32	3	1

Variants in ST6GALNAC1

This is a list of pathogenic ClinVar variants found in the ST6GALNAC1 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-76625353-C-T		not specified	Uncertain significance (Oct 25, 2022)
17-76625364-C-T		not specified	Uncertain significance (May 23, 2024)
17-76625365-G-T		not specified	Uncertain significance (Sep 27, 2022)
17-76625430-T-C		not specified	Uncertain significance (Mar 22, 2023)
17-76625439-A-G		not specified	Likely benign (Dec 18, 2023)
17-76625472-T-C		not specified	Uncertain significance (Aug 17, 2022)
17-76625475-T-C		not specified	Uncertain significance (May 10, 2022)
17-76625503-C-T		not specified	Uncertain significance (Aug 21, 2023)
17-76625505-G-T		not specified	Uncertain significance (Nov 06, 2023)
17-76625871-C-T		not specified	Uncertain significance (Dec 03, 2024)
17-76625907-G-C		not specified	Uncertain significance (Aug 15, 2023)
17-76626067-C-T		not specified	Uncertain significance (Nov 29, 2024)
17-76626308-T-C		not specified	Uncertain significance (Apr 24, 2024)
17-76626358-C-T		not specified	Uncertain significance (Aug 01, 2024)
17-76626665-C-T		not specified	Uncertain significance (Jul 28, 2021)
17-76626695-G-T		not specified	Uncertain significance (Dec 07, 2021)
17-76626719-C-T		not specified	Uncertain significance (Jun 29, 2023)
17-76626728-C-T		not specified	Uncertain significance (Feb 09, 2023)
17-76626742-C-T		not specified	Uncertain significance (Dec 04, 2024)
17-76626782-C-T		not specified	Uncertain significance (Aug 21, 2023)
17-76627128-C-T		not specified	Uncertain significance (Jul 21, 2021)
17-76627157-C-T		not specified	Likely benign (Dec 04, 2024)
17-76627158-G-A		not specified	Uncertain significance (Dec 27, 2022)
17-76627161-G-C		not specified	Uncertain significance (Apr 17, 2024)
17-76627191-G-T		ST6GALNAC1-related disorder	Likely benign (Jul 16, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ST6GALNAC1	protein_coding	protein_coding	ENST00000156626	9	19078

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.38e-11	0.331	125610	0	138	125748	0.000549

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.141	341	348	0.979	0.0000207	3907
Missense in Polyphen		97	106.22	0.91322		1204
Synonymous	0.0390	141	142	0.996	0.00000879	1204
Loss of Function	1.06	20	25.8	0.774	0.00000128	282

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00155	0.00155
Ashkenazi Jewish	0.00	0.00
East Asian	0.000326	0.000326
Finnish	0.000554	0.000554
European (Non-Finnish)	0.000536	0.000519
Middle Eastern	0.000326	0.000326
South Asian	0.000604	0.000588
Other	0.000388	0.000326

dbNSFP

Source: dbNSFP

• Pathway: Mucin type O-glycan biosynthesis - Homo sapiens (human);Globo Sphingolipid Metabolism;Post-translational protein modification;Metabolism of proteins;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;Asparagine N-linked glycosylation (Consensus)

Recessive Scores

• pRec: 0.105

Intolerance Scores

• loftool: 0.967
• rvis_EVS: 0.16
• rvis_percentile_EVS: 64.92

Haploinsufficiency Scores

• pHI: 0.114
• hipred: N
• hipred_score: 0.123
• ghis: 0.379

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.350

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: St6galnac1

Gene ontology

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