TMED7

Chr 5

transmembrane p24 trafficking protein 7

Also known as: CGI-109, Tag, p24g3, p24gamma3, p27

NCBI Gene: 51014 ENSG00000134970 UniProt: Q9Y3B3

Predicted to be involved in Golgi organization; endoplasmic reticulum to Golgi vesicle-mediated transport; and intracellular protein transport. Located in Golgi apparatus; endoplasmic reticulum; and endoplasmic reticulum-Golgi intermediate compartment. [provided by Alliance of Genome Resources, Jul 2025]

Research

ResearchGenerating clinical summary…

DNmechanismLOEUF 0.62

Clinical Summary— TMED7

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Population Constraint (gnomAD)

Constrained for loss-of-function variants (OE-LoF 0.20) despite low pLI — interpret in context.

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ClinVar Variants

56 VUS of 111 total submissions

Explore recent and relevant literature in Research Assistant →

Some data sources returned errors (1)

omim: Error: OMIM fetch failed: 429

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

0.62LOEUF

pLI 0.480

Z-score 2.37

OE 0.20 (0.08–0.62)

Tolerant

Typical tolerance to LoF variation

Missense Constraint?

1.50Z-score

OE missense 0.60 (0.49–0.74)

67 obs / 111.5 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?0.20 (0.08–0.62)

0≤0.351.4

Missense OE?0.60 (0.49–0.74)

0≤0.61.4

Synonymous OE?1.19

0≤1.21.6

LoF obs/exp: 2 / 10.2Missense obs/exp: 67 / 111.5Syn Z: -0.97

This gene — mechanism propensity

0.6356th %ile

GOF

0.6248th %ile

LOF

0.4234th %ile

The highest-scoring mechanism for this gene is dominant-negative.

DNprediction above median

Note: In-silico variant effect predictors (SIFT, PolyPhen, REVEL, CADD) may underestimate pathogenicity of missense variants in genes with GOF or DN mechanisms. Consider functional evidence and clinical context.

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

ClinVar Variant Classifications

111 submitted variants in ClinVar

ClinVar

Classification Summary

VUS56

Likely Benign48

Benign5

VUS

Likely Benign

Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

Classification	LoF	Missense + Inframe	Non-coding	Synonymous	Total
Pathogenic	0	0	0	0	0
Likely Pathogenic	0	0	0	0	0
VUS	2	51	3	0	56
Likely Benign	0	0	12	36	48
Benign	0	1	2	2	5
Total	2	52	17	38	109

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

View in ClinVar →

26 pathogenic / likely-pathogenic (of 31) ClinVar copy-number / structural variants overlap TMED7 — these span large chromosomal regions, not the gene specifically, and are excluded from the counts above. Explore in CNV tools →