SMG5

Chr 1

SMG5 nonsense mediated mRNA decay factor

Also known as: EST1B, LPTS-RP1, LPTSRP1, SMG-5

NCBI Gene: 23381ENSG00000198952UniProt: Q9UPR3OMIM: 610962

SMG5 is involved in nonsense-mediated mRNA decay (Ohnishi et al., 2003 [PubMed 14636577]).[supplied by OMIM, Mar 2008]

OMIMResearchGenerating clinical summary…
LOEUF 0.41
Clinical Summary— SMG5
⚡
Population Constraint (gnomAD)
Constrained for loss-of-function variants (OE-LoF 0.27) despite low pLI — interpret in context.
📋
ClinVar Variants
198 VUS of 254 total submissions
Explore recent and relevant literature in Research Assistant →

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Moderate LoF intolerance
LoF Constraint?
0.41LOEUF
pLI 0.013
Z-score 5.08
OE 0.27 (0.18–0.41)
Moderately constrained

More LoF-intolerant than ~75% of genes

Missense Constraint?
1.13Z-score
OE missense 0.87 (0.81–0.94)
510 obs / 586.9 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios?
LoF OE?0.27 (0.18–0.41)
0≤0.351.4
Missense OE?0.87 (0.81–0.94)
0≤0.61.4
Synonymous OE?1.02
0≤1.21.6
LoF obs/exp: 15 / 56.1Missense obs/exp: 510 / 586.9Syn Z: -0.23

ClinVar Variant Classifications

254 submitted variants in ClinVar

ClinVar

Classification Summary

VUS198
Likely Benign12
Benign6
198
VUS
12
Likely Benign
6
Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
0
0
0
0
Likely Pathogenic
0
0
0
0
0
VUS
0
198
0
0
198
Likely Benign
0
8
0
4
12
Benign
0
3
1
2
6
Total020916216

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

View in ClinVar →

19 pathogenic / likely-pathogenic (of 27) ClinVar copy-number / structural variants overlap SMG5 — these span large chromosomal regions, not the gene specifically, and are excluded from the counts above. Explore in CNV tools →

Protein Context — Lollipop Plot

SMG5 · protein map & ClinVar variants

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

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

Search ClinicalTrials.gov →

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