TONSL p.Gly486Val
c.1457_1458delinsTT · rs1823644466 · VCV1004635
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Not reported
no gnomAD frequency available for this variant
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -3.9 | GERP -3.9 |
| Regional constraint | o/e 1.01 | unconstrained · MANE · 15 kb · p 0.67 · regional, not allelic |
| Region caveats | ||
| Repeat context | tandem | (CTCCGC)n simple repeat · ambiguous alignment · confidence, not pathogenicity |
Population frequency
dbSNP / gnomAD
No gnomAD frequency available for this variant. This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.
Variant & gene context
- Gene
- TONSL
- Protein
- p.Gly486Val
- Coding
- c.1457_1458delinsTT
- MANE Select
- NM_013432
- dbSNP
- rs1823644466
- Type
- Indel
- Location
- chr8:144440043 (GRCh38)
- Gene constraint
- LOEUF 1.024 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 76.06 · 3 PDB
- Residue 486
- the 'disordered' region; a UniProt-annotated variant site (in semdsp; disease phenotype includes immunologic and hematologic abnormalities); a UniProt-annotated variant site (in semdsp)
Similar variants
- TONSL p.Gly486= Benign ★★ same residue
- TONSL p.Gly486Arg Uncertain significance ★ ⚠ same residue
- TONSL p.Gly486Ser Conflicting classifications of pathogenicity ★ ⚠ same residue
- TONSL p.Ala985fs Likely pathogenic ★ same type
- TONSL c.865+15_865+16delinsCG Uncertain significance ★ same type
- TONSL c.865+15_865+16delinsCT Uncertain significance ★ same type
- TONSL p.Glu156Leu Uncertain significance ★ same type
- TONSL p.Pro1204Tyr Uncertain significance ★ same type
Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →
Cite Sugi Variant
Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/tonsl-p-gly486val (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown