TRAPPC10

Chr 21

trafficking protein particle complex subunit 10

Also known as: EHOC-1, EHOC1, GT334, NEDMISS, TMEM1, TRS130, TRS30

NCBI Gene: 7109 ENSG00000160218 UniProt: P48553

The encoded transmembrane protein is a specific subunit of the TRAPP II complex that functions as a membrane tether in vesicular transport from the endoplasmic reticulum through the Golgi apparatus. Mutations cause autosomal recessive neurodevelopmental disorder with microcephaly, short stature, and speech delay. This gene is highly constrained against loss-of-function variants (pLI ~1.0, LOEUF 0.204), indicating that functional copies are essential for normal development.

ResearchSummary from RefSeq, OMIM, UniProt

The protein encoded by this gene is a transmembrane protein found in the cis-Golgi complex. The encoded protein is part of the multisubunit transport protein particle (TRAPP) complex and may be involved in vesicular transport from the endoplasmic reticulum to the Golgi. Mutations in this gene could be responsible for the Unverricht-Lundborg type of progressive myoclonus epilepsy, or for autoimmune polyglandular disease type 1. [provided by RefSeq, Jul 2008]

ResearchGenerating clinical summary…

LOFmechanismLOEUF 0.20

Clinical Summary— TRAPPC10

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Population Constraint (gnomAD)

Highly constrained gene — heterozygous loss-of-function variants are very rare in the population (pLI 1.00). One damaged copy is likely sufficient to cause disease.

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ClinVar Variants

6 unique Pathogenic / Likely Pathogenic· 156 VUS of 210 total submissions

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Some data sources returned errors (1)

omim: Error: OMIM fetch failed: 429

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

LoF intolerant — likely haploinsufficient

LoF Constraint?

0.20LOEUF

pLI 1.000

Z-score 6.63

OE 0.11 (0.06–0.20)

Highly constrained

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

Missense Constraint?

1.56Z-score

OE missense 0.84 (0.78–0.89)

600 obs / 717.7 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?0.11 (0.06–0.20)

0≤0.351.4

Missense OE?0.84 (0.78–0.89)

0≤0.61.4

Synonymous OE?1.01

0≤1.21.6

LoF obs/exp: 7 / 64.4Missense obs/exp: 600 / 717.7Syn Z: -0.11

Curated Mechanism (G2P)Gene2Phenotype (DDG2P) ↗

limitedTRAPPC10-related intellectual disabilityOTHERAR

This gene — mechanism propensity

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

0.2499th %ile

GOF

0.2198th %ile

LOF

0.75top 10%

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. Mechanism ranking also informed by gnomAD constraint, ClinVar, and ClinGen data.

ClinVar Variant Classifications

210 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic1

Likely Pathogenic5

VUS156

Likely Benign20

Benign1

Pathogenic

Likely Pathogenic

156

VUS

Likely Benign

Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

Classification	LoF	Missense + Inframe	Non-coding	Synonymous	Total
Pathogenic	1	0	0	0	1
Likely Pathogenic	4	1	0	0	5
VUS	0	154	2	0	156
Likely Benign	0	11	1	8	20
Benign	0	0	1	0	1
Total	5	166	4	8	183

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

View in ClinVar →

91 pathogenic / likely-pathogenic (of 112) ClinVar copy-number / structural variants overlap TRAPPC10 — these span large chromosomal regions, not the gene specifically, and are excluded from the counts above. Explore in CNV tools →