ST6GALNAC6

Chr 9

ST6 N-acetylgalactosaminide alpha-2,6-sialyltransferase 6

Also known as: SIAT7-F, SIAT7F, ST6GALNACVI

NCBI Gene: 30815 ENSG00000160408 UniProt: Q969X2 OMIM: 610135

ST6GALNAC6 encodes a sialyltransferase that transfers sialyl groups to glycoproteins and glycolipids with alpha-2,6-linkage specificity, particularly catalyzing ganglioside GD1alpha biosynthesis from GM1b and other complex glycolipid modifications. The gene shows low constraint to loss-of-function variation (pLI 0.002, LOEUF 0.815), and no definitive human disease associations have been established from the provided data.

OMIM ResearchSummary from RefSeq, UniProt

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]

OMIM ResearchGenerating clinical summary…

Active trials

Pubs (1 yr)

—

P/LP submissions

—

P/LP missense

0.81

LOEUF

—

Mechanism

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

0.81LOEUF

pLI 0.002

Z-score 2.11

OE 0.43 (0.25–0.81)

Tolerant

Typical tolerance to LoF variation

Missense Constraint?

1.57Z-score

OE missense 0.71 (0.63–0.81)

166 obs / 233.4 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?0.43 (0.25–0.81)

0≤0.351.4

Missense OE?0.71 (0.63–0.81)

0≤0.61.4

Synonymous OE?1.02

0≤1.21.6

LoF obs/exp: 7 / 16.1Missense obs/exp: 166 / 233.4Syn Z: -0.14

Background carrier burden — how many people carry a rare variant somewhere in ST6GALNAC6?

gnomAD v4 · ~731k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 76

504 rare PASS variants

Rare truncating (LoF)

1 in 790

77 rare PASS variants

Rare synonymous (reference)

1 in 280

185 rare PASS variants

Truncating variants are far rarer here than missense — that gap, in human units, is what constraint means for ST6GALNAC6. A background rate for each class, not the frequency of any particular variant; thin-coverage exons undercount.

By genetic ancestry · 9 gnomAD groups · rare = under 0.1% in that group

Group	People	Missense	Truncating
European (non-Finnish)	~556k	1 in 110	1 in 1,200
South Asian	~43k	1 in 150	1 in 770
Remaining (unassigned)	~30k	1 in 65	1 in 550
European (Finnish)	~27k	1 in 380	1 in 1,300
Admixed American	~22k	1 in 100	1 in 2,500
African / African American	~21k	1 in 59	1 in 290
East Asian	~20k	1 in 99	1 in 2,800
Ashkenazi Jewish	~13k	1 in 440	none seen
Middle Eastern	~2,884	1 in 74	≈ 1 in 1,400

Each group is summed over the variants that are rare in that group. Grey ≈ figures rest on fewer than five expected carriers — too few to distinguish groups. Differences mostly reflect how many people were sampled and how much variation each ancestry carries, not disease risk.

Exome coverage (gnomAD): 5 of 6 coding exons well covered in gnomAD exomes; exon 2 marginal. Genomes: all 6.? see exons ↓