ST6GALNAC5

protein-coding

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

Gene summary

The protein encoded by this gene is a Golgi type II transmembrane glycosyltransferase. The encoded protein catalyzes the transfer of sialic acid to cell surface proteins to modulate cell-cell interactions. Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Feb 2016]

Previous symbols:

SIAT7E

MANE transcript

NM_030965.3

Inheritance

—

ClinVar variants

P:1U:57B:1

Top phenotype

Hypercholesterolemia, familial, 1

gnomAD constraint

pLI —, LoF o/e 0.27

Max pathogenic AF

—

Genomic locus

chr1:76,867,480-77,067,546

External References & Databases

Ensembl (ENSG00000117069)

Transcript & Mutation Effects

hg38 • Region Span ~200.1 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 ST6GALNAC5 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 55

not providedTotal: 2

Hypercholesterolemia, familial, 1Total: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_030965.3. 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			56 clinvar			56
nonsense						0
start loss						0
frameshift	1 clinvar					1
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	1	0	57	0	1	59

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 17 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_030965.3	RefSeq	NP_112227.1	5	MANE Select
ENST00000477717.6	Ensembl	ENSP00000417583.1	5	MANE Select
NM_001320273.2	RefSeq	NP_001307202.1	3	Standard
NM_001320274.2	RefSeq	NP_001307203.1	3	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

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

Biological Process

protein glycosylation
glycosphingolipid biosynthetic process
oligosaccharide biosynthetic process
sialylation

Molecular Function

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

Cellular Component

Golgi membrane
integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000477717
Coding exons: 5
Length: 198271
Individuals with no LoFs: 125727
Homozygous LoFs: 0
Heterozygous LoFs: 21
Defined: 125748
p: 0.0000835

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.541	185	207	0.894	0.0000120	2215
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00015	0.00012	rare
Latino/Admixed American	0.00014	0.00014	rare
Ashkenazi Jewish	0.00010	0.000099	rare
East Asian	0.00016	0.00016	rare
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.000056	0.000044	rare
South Asian	0.00016	0.00013	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

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}.;

Recessive Scores

pRec: 0.113

Intolerance Scores

LoFtool: 0.306
RVIS EVS: -0.47
RVIS percentile EVS: 23.04

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.262

Gene Damage Prediction

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