ALG9

Chr 11AR

ALG9 alpha-1,2-mannosyltransferase

Also known as: CDG1L, DIBD1, GIKANIS, LOH11CR1J

NCBI Gene: 79796ENSG00000086848UniProt: Q9H6U8OMIM: 606941

The protein is an alpha-1,2-mannosyltransferase enzyme that functions in lipid-linked oligosaccharide assembly in the endoplasmic reticulum membrane. Mutations cause congenital disorder of glycosylation type Il and Gillessen-Kaesbach-Nishimura syndrome through autosomal recessive inheritance. The pathogenic mechanism involves disruption of the glycosylation pathway due to defective oligosaccharide assembly.

GeneReviewsOMIMResearchSummary from RefSeq, OMIM, UniProt
LOFmechanismARLOEUF 0.652 OMIM phenotypes
Clinical Summary— ALG9
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Gene-Disease Validity (ClinGen)
ALG9-associated autosomal dominant polycystic kidney disease · ADDefinitive

Definitive — sufficient evidence for diagnostic panels

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Population Constraint (gnomAD)
Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.
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ClinVar Variants
56 unique Pathogenic / Likely Pathogenic· 183 VUS of 427 total submissions
Explore recent and relevant literature in Research Assistant →
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GeneReview available — ALG9
Authoritative clinical overview · Recommended first read
Open GeneReview ↗

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Tolerant — LoF & missense variants common in population
LoF Constraint
0.65LOEUF
pLI 0.001
Z-score 2.91
OE 0.38 (0.24–0.65)
Tolerant

Typical tolerance to LoF variation

Missense Constraint
1.01Z-score
OE missense 0.81 (0.72–0.92)
190 obs / 233.4 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios
LoF OE0.38 (0.24–0.65)
0≤0.351.4
Missense OE0.81 (0.72–0.92)
0≤0.61.4
Synonymous OE0.95
0≤1.21.6
LoF obs/exp: 10 / 26.0Missense obs/exp: 190 / 233.4Syn Z: 0.37
Curated Mechanism (G2P)Gene2Phenotype (DDG2P) ↗
strongALG9-related congenital disorder of glycosylationLOFAR

Predictions shown for reference only — model trained on dominant genes, not applicable to AR conditions.

DN
0.6260th %ile
GOF
0.5269th %ile
LOF
0.3355th %ile

The Badonyi & Marsh prediction model was trained exclusively on dominant disease genes. Predictions are not reliable for genes with autosomal recessive inheritance and are shown at reduced opacity for reference only.

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

ClinVar Variant Classifications

427 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic32
Likely Pathogenic24
VUS183
Likely Benign124
Benign33
Conflicting16
32
Pathogenic
24
Likely Pathogenic
183
VUS
124
Likely Benign
33
Benign
16
Conflicting

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
11
2
19
0
32
Likely Pathogenic
21
2
1
0
24
VUS
4
105
69
5
183
Likely Benign
0
6
64
54
124
Benign
0
4
29
0
33
Conflicting
—16
Total3611918259412

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

View in ClinVar →

Protein Context — Lollipop Plot

ALG9 · 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 ↗
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