TRAPPC2L

Chr 16AR

trafficking protein particle complex subunit 2L

Also known as: HSPC176, PERRB

NCBI Gene: 51693 ENSG00000167515 UniProt: Q9UL33 OMIM: 610970

This gene encodes a protein that interacts with the TRAPP complex to mediate vesicular transport from the endoplasmic reticulum to Golgi apparatus. Mutations cause progressive early-onset encephalopathy with episodic rhabdomyolysis, inherited in an autosomal recessive pattern. The gene is not highly constrained against loss-of-function variants in the general population.

OMIM ResearchSummary from RefSeq, OMIM, UniProt

This gene encodes a protein that interacts with the tethering factor trafficking protein particle (TRAPP complex). TRAPP complexes mediate the contact between vescicles and target membranes, and thus, are involved in vescicle-mediated transport of proteins and lipids. The encoded protein is related to the X-linked trafficking protein particle complex 2. A related pseudogene is located on the X chromosome. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Jan 2016]

OMIM ResearchGenerating clinical summary…

ARLOEUF 1.951 OMIM phenotype

Clinical Summary— TRAPPC2L

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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

24 unique Pathogenic / Likely Pathogenic· 68 VUS of 183 total submissions

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Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

1.95LOEUF

pLI 0.000

Z-score -1.69

OE 1.65 (1.02–1.95)

Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint?

-0.38Z-score

OE missense 1.11 (0.95–1.31)

102 obs / 91.7 exp

Tolerant

Tolerant to missense variation

Observed / Expected Ratios?

LoF OE?1.65 (1.02–1.95)

0≤0.351.4

Missense OE?1.11 (0.95–1.31)

0≤0.61.4

Synonymous OE?1.45

0≤1.21.6

LoF obs/exp: 13 / 7.9Missense obs/exp: 102 / 91.7Syn Z: -2.20

ClinVar Variant Classifications

183 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic15

Likely Pathogenic9

VUS68

Likely Benign56

Benign11

Conflicting9

Pathogenic

Likely Pathogenic

VUS

Likely Benign

Benign

Conflicting

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

Classification	LoF	Missense + Inframe	Non-coding	Synonymous	Total
Pathogenic	9	4	2	0	15
Likely Pathogenic	4	5	0	0	9
VUS	0	60	7	1	68
Likely Benign	0	4	19	33	56
Benign	0	4	5	2	11
Conflicting	—				9
Total	13	77	33	36	168

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

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69 pathogenic / likely-pathogenic (of 93) ClinVar copy-number / structural variants overlap TRAPPC2L — these span large chromosomal regions, not the gene specifically, and are excluded from the counts above. Explore in CNV tools →