STT3B

Chr 3

STT3 oligosaccharyltransferase complex catalytic subunit B

Also known as: CDG1X, SIMP, STT3-B

NCBI Gene: 201595 ENSG00000163527 UniProt: Q8TCJ2

STT3B encodes a catalytic subunit of the oligosaccharyl transferase complex that transfers oligosaccharides to asparagine residues during protein N-glycosylation in the endoplasmic reticulum. Mutations cause congenital disorder of glycosylation type Ix, inherited in an autosomal recessive pattern. The gene is highly constrained against loss-of-function variants, indicating that complete loss of function is likely incompatible with normal development.

ResearchSummary from RefSeq, OMIM, UniProt

The protein encoded by this gene is a catalytic subunit of a protein complex that transfers oligosaccharides onto asparagine residues. Defects in this gene are a cause of congenital disorder of glycosylation Ix (CDG1X). [provided by RefSeq, Jun 2014]

ResearchGenerating clinical summary…

Primary Disease Associations & Inheritance

UniProtCongenital disorder of glycosylation 1X

Clinical highlights

Gene–disease validity (ClinGen)

Limited · congenital disorder of glycosylation · AR · ClinGen 2026

not for standalone diagnostic reporting

Interpreting a novel variant

Loss of function is the curated mechanism (Gene2Phenotype) and the gene is intolerant of it in the population — truncating, frameshift and canonical splice variants carry more prior weight here than missense.Curated gene-level mechanism — a prior for triage, not a per-variant call.

Active trials

Pubs (1 yr)

—

P/LP submissions

—

P/LP missense

0.25

LOEUF· LoF intol.

LOF

Mechanism· G2P

Some data sources returned errors (1)

omim: Error: OMIM fetch failed: 429

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Dual constrained — LoF & missense intolerant

LoF Constraint?

0.25LOEUF

pLI 0.999

Z-score 5.29

OE 0.12 (0.06–0.25)

Highly constrained

Highly LoF-intolerant (top ~10% of genes)

Missense Constraint?

3.76Z-score

OE missense 0.49 (0.43–0.55)

205 obs / 422.2 exp

Constrained

Highly missense-constrained (top ~0.1%)

Observed / Expected Ratios?

LoF OE?0.12 (0.06–0.25)

0≤0.351.4

Missense OE?0.49 (0.43–0.55)

0≤0.61.4

Synonymous OE?1.02

0≤1.21.6

LoF obs/exp: 5 / 42.0Missense obs/exp: 205 / 422.2Syn Z: -0.18

Background carrier burden — how many people carry a rare variant somewhere in STT3B?

gnomAD v4 · ~731k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 170

691 rare PASS variants

Rare truncating (LoF)

1 in 5,500

59 rare PASS variants

Rare synonymous (reference)

1 in 250

396 rare PASS variants

Truncating variants are far rarer here than missense — that gap, in human units, is what constraint means for STT3B. 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 190	1 in 4,600
South Asian	~43k	1 in 160	1 in 3,100
Remaining (unassigned)	~30k	1 in 150	≈ 1 in 7,100
European (Finnish)	~27k	1 in 490	1 in 5,300
Admixed American	~22k	1 in 170	1 in 3,300
African / African American	~21k	1 in 130	1 in 2,700
East Asian	~20k	1 in 160	≈ 1 in 6,000
Ashkenazi Jewish	~13k	1 in 760	none seen
Middle Eastern	~2,884	1 in 150	none seen

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): 11 of 16 coding exons well covered in gnomAD exomes; exons 1, 2, 5, 8, 14 marginal. Genomes: all 16.? see exons ↓