TBC1D32 p.Leu1237=
c.3711G>A · rs2128164851 · VCV1383946
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 4.8 | GERP 1.7, phastCons 1 |
| Overall | ||
| CADD | 9.499 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- TBC1D32
- Protein
- p.Leu1237=
- Coding
- c.3711G>A
- MANE Select
- NM_152730
- dbSNP
- rs2128164851
- Type
- single nucleotide variant
- Location
- chr6:121080834 (GRCh38)
- Gene constraint
- LOEUF 0.984 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 80.84
- Residue 1237
- the rab-gap tbc domain; a UniProt-annotated variant site (in rp100; likely pathogenic)
Similar variants
- TBC1D32 p.Arg734Ter Pathogenic/Likely pathogenic ★★ same type
- TBC1D32 p.Arg1104Thr Uncertain significance ★★ ⚠ same type
- TBC1D32 p.Arg135Gln Uncertain significance ★★ ⚠ same type
- TBC1D32 p.Arg287Cys Uncertain significance ★★ ⚠ same type
- TBC1D32 p.Arg287His Uncertain significance ★★ ⚠ same type
- TBC1D32 p.Arg820Cys Uncertain significance ★★ ⚠ same type
- TBC1D32 p.Arg884Trp Uncertain significance ★★ ⚠ same type
- TBC1D32 p.Asp661Val 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/tbc1d32-p-leu1237 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown