TRAPPC9

Chr 8AR

trafficking protein particle complex subunit 9

Also known as: IBP, IKBKBBP, MRT13, NIBP, T1, TRS120

NCBI Gene: 83696ENSG00000167632UniProt: Q96Q05OMIM: 611966

The protein encoded by this gene localizes to the Golgi apparatus and cis-Golgi network and likely functions in NF-kappa-B signaling. Mutations cause autosomal recessive intellectual developmental disorder (type 13). The inheritance pattern is autosomal recessive.

OMIMResearchSummary from RefSeq, OMIM, UniProt
LOFmechanismARLOEUF 0.731 OMIM phenotype
Clinical Summary— TRAPPC9
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Gene-Disease Validity (ClinGen)
intellectual disability-obesity-brain malformations-facial dysmorphism syndrome · ARDefinitive

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
49 unique Pathogenic / Likely Pathogenic· 192 VUS of 500 total submissions
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Clinical Trials
1 active or recruiting trial — potential therapeutic options may be available
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
0.73LOEUF
pLI 0.000
Z-score 3.23
OE 0.55 (0.41–0.73)
Tolerant

Typical tolerance to LoF variation

Missense Constraint
1.48Z-score
OE missense 0.85 (0.79–0.91)
626 obs / 739.2 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios
LoF OE0.55 (0.41–0.73)
0≤0.351.4
Missense OE0.85 (0.79–0.91)
0≤0.61.4
Synonymous OE1.12
0≤1.21.6
LoF obs/exp: 32 / 58.7Missense obs/exp: 626 / 739.2Syn Z: -1.64

ClinVar Variant Classifications

500 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic33
Likely Pathogenic16
VUS192
Likely Benign222
Benign3
Conflicting1
33
Pathogenic
16
Likely Pathogenic
192
VUS
222
Likely Benign
3
Benign
1
Conflicting

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
19
0
14
0
33
Likely Pathogenic
14
0
2
0
16
VUS
2
169
19
2
192
Likely Benign
0
6
93
123
222
Benign
0
0
2
1
3
Conflicting
—1
Total35175130126467

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

View in ClinVar →

Protein Context — Lollipop Plot

TRAPPC9 · protein map & ClinVar variants

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

3D Protein StructureAlphaFold
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 5 results · since 2015Search PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
Canine Neuronal Ceroid Lipofuscinosis-like Disorder Associated with Sequence Variants in AP3B1 and TRAPPC9.
Then A et al.·Genes (Basel)
2025Open Access
Overexpression of ZFP69B promotes hepatocellular carcinoma growth by upregulating the expression of TLX1 and TRAPPC9.
Xie W et al.·Cell Div
2024Open Access
Case Report: Whole exome sequencing identifies compound heterozygous variants in the TRAPPC9 gene in a child with developmental delay.
Yu B et al.·Front Genet
2024Open AccessCase report
Chronic pharmacologic manipulation of dopamine transmission ameliorates metabolic disturbance in Trappc9-linked brain developmental syndrome.
Li Y et al.·JCI Insight
2024Open Access
Expanding the genetic and phenotypic spectrum of TRAPPC9 and MID2-related neurodevelopmental disabilities: report of two novel mutations, 3D-modelling, and molecular docking studies.
Kharrat M et al.·J Hum Genet
2024Functional
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