TRAPPC9

Chr 8AR

trafficking protein particle complex subunit 9

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

NCBI Gene: 83696 ENSG00000167632 UniProt: Q96Q05 OMIM: 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.

OMIM ResearchSummary from RefSeq, OMIM, UniProt

This gene encodes a protein that likely plays a role in NF-kappa-B signaling. Mutations in this gene have been associated with autosomal-recessive cognitive disability. Alternatively spliced transcript variants have been described.[provided by RefSeq, Feb 2010]

OMIM ResearchGenerating clinical summary…

Primary Disease Associations & Inheritance

Intellectual developmental disorder, autosomal recessive 13MIM #613192

Clinical highlights

Gene–disease validity (ClinGen)

Definitive · intellectual disability-obesity-brain malformations-facial dysmorphism syndrome · AR · ClinGen 2020

Interpreting a novel variant

Loss of function is the curated mechanism (Gene2Phenotype), though the gene is not strongly LoF-constrained in the population — weigh truncating variants against that tolerance.Curated gene-level mechanism — a prior for triage, not a per-variant call.

Active trials

Pubs (1 yr)

—

P/LP submissions

—

P/LP missense

0.73

LOEUF

LOF

Mechanism· G2P

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 OE?0.55 (0.41–0.73)

0≤0.351.4

Missense OE?0.85 (0.79–0.91)

0≤0.61.4

Synonymous OE?1.12

0≤1.21.6

LoF obs/exp: 32 / 58.7Missense obs/exp: 626 / 739.2Syn Z: -1.64

Background carrier burden — how many people carry a rare variant somewhere in TRAPPC9?

gnomAD v4 · ~731k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 31

1,396 rare PASS variants

Rare truncating (LoF)

1 in 970

163 rare PASS variants

Rare synonymous (reference)

1 in 41

674 rare PASS variants

Truncating variants are far rarer here than missense — that gap, in human units, is what constraint means for TRAPPC9. 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 43	1 in 950
South Asian	~43k	1 in 35	1 in 2,100
Remaining (unassigned)	~30k	1 in 25	1 in 1,500
European (Finnish)	~27k	1 in 120	≈ 1 in 13,000
Admixed American	~22k	1 in 44	1 in 530
African / African American	~21k	1 in 38	1 in 1,200
East Asian	~20k	1 in 42	1 in 1,800
Ashkenazi Jewish	~13k	1 in 77	≈ 1 in 6,500
Middle Eastern	~2,884	1 in 31	≈ 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): All 22 coding exons well covered in gnomAD exomes and genomes.? see exons ↓