STON1-GTF2A1L

Chr 2

STON1-GTF2A1L readthrough

Also known as: SALF

NCBI Gene: 286749ENSG00000068781

This gene produces read-through fusion transcripts combining stonin 1 (involved in endocytic trafficking) and general transcription factor IIA-like proteins, though the function of the resulting fusion protein remains undetermined. The gene shows extremely low constraint against loss-of-function variants (pLI near zero), and no established disease associations have been reported for mutations in this read-through gene product.

Summary from RefSeq
Research Assistant →
0
Active trials
0
Pubs (1 yr)
108
P/LP submissions
46%
P/LP missense
1.09
LOEUF
—
Mechanism
Clinical Summary— STON1-GTF2A1L
⚡
Population Constraint (gnomAD)
Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.
📋
ClinVar Variants
68 unique Pathogenic / Likely Pathogenic· 199 VUS of 396 total submissions
Explore recent and relevant literature in Research Assistant →

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Tolerant — LoF & missense variants common in population
LoF Constraint
1.09LOEUF
pLI 0.000
Z-score 1.03
OE 0.83 (0.64–1.09)
Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint
-2.79Z-score
OE missense 1.32 (1.25–1.40)
779 obs / 588.5 exp
Tolerant

Tolerant to missense variation

Observed / Expected Ratios
LoF OE0.83 (0.64–1.09)
0≤0.351.4
Missense OE1.32 (1.25–1.40)
0≤0.61.4
Synonymous OE1.21
0≤1.21.6
LoF obs/exp: 38 / 45.5Missense obs/exp: 779 / 588.5Syn Z: -2.44

ClinVar Variant Classifications

396 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic45
Likely Pathogenic23
VUS199
Likely Benign51
Benign47
Conflicting28
45
Pathogenic
23
Likely Pathogenic
199
VUS
51
Likely Benign
47
Benign
28
Conflicting

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
6
21
18
0
45
Likely Pathogenic
7
10
6
0
23
VUS
0
163
34
2
199
Likely Benign
0
7
28
16
51
Benign
0
3
40
4
47
Conflicting
—28
Total1320412622393

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

View in ClinVar →

Protein Context — Lollipop Plot

STON1-GTF2A1L · 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