TBC1D23 p.Ile245=
c.735T>C · rs199967519 · VCV3042314
Benign
No assertion criteria
Classification
Benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
low-frequency (popmax 2.79%, sas)
Conditions
1
TBC1D23-related disorder
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 5.1 | GERP 0.57, phastCons 1 |
| Overall | ||
| CADD | 11.08 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
2.79%
South Asian · 2,521/90,338 alleles
Filtering AF
2.7%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 2.66%
Overall
0.167%
2,693/1,610,940 alleles · low-frequency
exomes 2,538/1,458,604 · genomes 155/152,336 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 2.79% | 36 |
| Remaining individualsnot grpmax-eligible | 0.194% | 515 |
| Middle Eastern | 0.0855% | 1,169 |
| Admixed American | 0.0101% | 9,921 |
| East Asian | 0.0067% | 14,919 |
| African / African-American | 0.00401% | 24,965 |
| European (non-Finnish) | 0.00288% | 34,670 |
Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.
Variant & gene context
- Gene
- TBC1D23
- Protein
- p.Ile245=
- Coding
- c.735T>C
- MANE Select
- NM_001199198
- dbSNP
- rs199967519
- Type
- single nucleotide variant
- Location
- chr3:100295311 (GRCh38)
- Gene constraint
- LOEUF 0.882 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 80.69 · 4 PDB
- Residue 245
- an α-helix
Disease context
TBC1D23-related disorder
Similar variants
- TBC1D23 c.1306+3A>G Uncertain significance ★ same condition
- TBC1D23 p.Gly448Arg Uncertain significance same condition
- TBC1D23 c.1554-4A>G Likely benign same condition
- TBC1D23 p.Glu181= Likely benign same condition
- TBC1D23 p.Ile671= Likely benign same condition
- TBC1D23 p.Leu204= Likely benign same condition
- TBC1D23 p.Ser300Thr Benign same condition
- TBC1D23 p.Ala417fs Likely pathogenic same condition
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/tbc1d23-p-ile245 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown