ST6GALNAC6

protein-coding

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

Gene summary

ST6GALNAC6 belongs to a family of sialyltransferases that modify proteins and ceramides on the cell surface to alter cell-cell or cell-extracellular matrix interactions (Tsuchida et al., 2003 [PubMed 12668675]).[supplied by OMIM, Mar 2008]

Previous symbols:

SIAT7F

MANE transcript

NM_013443.5

Inheritance

—

ClinVar variants

U:47B:1

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.43

Max pathogenic AF

—

Genomic locus

chr9:127,885,321-127,905,408

External References & Databases

Ensembl (ENSG00000160408)

Transcript & Mutation Effects

hg38 • Region Span ~20.1 kb

Loading mutation effect viewer...

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 ST6GALNAC6 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 42

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_013443.5. 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	1 clinvar		43
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			3 clinvar			3
Total	0	0	47	1	0	48

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 57 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_013443.5	RefSeq	NP_038471.2	6	MANE Select
ENST00000373146.6	Ensembl	ENSP00000362239.1	6	MANE Select
NM_001286999.2	RefSeq	NP_001273928.1	6	Standard
NM_001287000.2	RefSeq	NP_001273929.1	5	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Glycosphingolipid biosynthesis - ganglio series - Homo sapiens (human)
Ganglio Sphingolipid Metabolism
Globo Sphingolipid Metabolism
Post-translational protein modification
Metabolism of proteins

Biological Process

ganglioside biosynthetic process
protein glycosylation
glycosylceramide metabolic process
glycosphingolipid metabolic process
glycoprotein metabolic process

Molecular Function

alpha-N-acetylgalactosaminide alpha-2,6-sialyltransferase activity
sialyltransferase activity

Cellular Component

Golgi membrane
cytoplasm
plasma membrane
integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000373146
Coding exons: 6
Length: 20088
Individuals with no LoFs: 125736
Homozygous LoFs: 0
Heterozygous LoFs: 9
Defined: 125745
p: 0.0000358

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.57	166	233	0.711	0.0000158	2172
Missense (PolyPhen)		40	81.051	0.49352		788
Synonymous	-0.141	95	93.3	1.02	0.00000616	679
Loss of Function	2.11	7	16.1	0.434	9.41e-7	160

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000029	0.000029	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00011	0.00011	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000053	0.000053	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Alpha-2,6-sialyltransferase involved in the synthesis of alpha-series gangliosides. Has activity toward GD1a, GT1b and GM1b. Has no activity toward glycoproteins. Responsible for the biosynthesis of DSGG (disialylgalactosylgloboside) from MSGG (monosialylgalactosylgloboside) in normal and malignant kidney. Participates in the synthesis of disialyl Lewis a (Le(a)). {ECO:0000269|PubMed:12668675, ECO:0000269|PubMed:17123352}.;

Recessive Scores

pRec: 0.0931

Intolerance Scores

RVIS EVS: -1.02
RVIS percentile EVS: 7.94

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.365

Gene Damage Prediction

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