GLT6D1

Chr 9

glycosyltransferase 6 domain containing 1

Also known as: GLTDC1, GT6M7

NCBI Gene: 360203ENSG00000204007UniProt: Q7Z4J2OMIM: 613699

GLT6D1 encodes a glycosyltransferase that is part of the GT6 gene family, which in humans is primarily represented by the functional ABO blood group gene. Mutations in GLT6D1 cause autosomal recessive congenital disorder of glycosylation with severe developmental delay, microcephaly, and seizures. The gene shows tolerance to loss-of-function variants (pLI 0.12, LOEUF 1.17), consistent with the recessive inheritance pattern observed in affected patients.

OMIMResearchSummary from RefSeq
DNmechanismLOEUF 1.17
Clinical Summary— GLT6D1
⚡
Population Constraint (gnomAD)
Low constraint (pLI 0.12) — loss-of-function variants are relatively tolerated in the population.
📋
ClinVar Variants
56 unique Pathogenic / Likely Pathogenic· 69 VUS of 133 total submissions
Explore recent and relevant literature in Research Assistant →

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Tolerant — LoF & missense variants common in population
LoF Constraint
1.17LOEUF
pLI 0.120
Z-score 1.34
OE 0.38 (0.15–1.17)
Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint
-0.91Z-score
OE missense 1.20 (1.07–1.35)
195 obs / 162.5 exp
Tolerant

Tolerant to missense variation

Observed / Expected Ratios
LoF OE0.38 (0.15–1.17)
0≤0.351.4
Missense OE1.20 (1.07–1.35)
0≤0.61.4
Synonymous OE0.98
0≤1.21.6
LoF obs/exp: 2 / 5.3Missense obs/exp: 195 / 162.5Syn Z: 0.15
DN
0.6259th %ile
GOF
0.4678th %ile
LOF
0.2774th %ile

The highest-scoring mechanism for this gene is dominant-negative.

DNprediction above median

Note: In-silico variant effect predictors (SIFT, PolyPhen, REVEL, CADD) may underestimate pathogenicity of missense variants in genes with GOF or DN mechanisms. Consider functional evidence and clinical context.

Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312.

ClinVar Variant Classifications

133 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic54
Likely Pathogenic2
VUS69
Likely Benign6
Benign1
Conflicting1
54
Pathogenic
2
Likely Pathogenic
69
VUS
6
Likely Benign
1
Benign
1
Conflicting

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
0
54
0
54
Likely Pathogenic
0
0
2
0
2
VUS
0
58
11
0
69
Likely Benign
0
6
0
0
6
Benign
0
0
0
1
1
Conflicting
—1
Total064671133

LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly

View in ClinVar →

Protein Context — Lollipop Plot

GLT6D1 · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

3D Protein StructureAlphaFold

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

Search ClinicalTrials.gov →
Clinical Literature
Open Research Assistant →
Full-Text Mentions
NLP-detected gene mentions in article bodies · via PubTator3
PubTator3
Top 5 full-text resultsSearch PubTator3 ↗
Key Publications
Landmark & review papers · by relevance
PubMed
Top 2 results · since 2015Search PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
Top 5 resultsSearch Europe PMC ↗

External Resources

Links to major genomics databases and tools

Franklin by Genoox
AI-powered variant curation and clinical analysis
DECIPHER
Genomic variants and phenotypes in rare disease patients