TBCD p.Ser923=
c.2769C>T · rs771565807 · VCV2701398
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0703%, sas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · C>G here scores Δ0.20 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -11 | GERP -2.7 |
| Overall | ||
| CADD | 0.494 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0703%
South Asian · 64/91,078 alleles
Filtering AF
0.0565%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0514%
Overall
0.00558%
90/1,613,854 alleles · ultra-rare
exomes 90/1,461,560 · genomes 0/152,294 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0703% | 1,423 |
| Remaining individualsnot grpmax-eligible | 0.0208% | 4,807 |
| Middle Eastern | 0.0165% | 6,062 |
| Admixed American | 0.00167% | 60,026 |
| European (non-Finnish) | 0.000932% | 107,263 |
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
- TBCD
- Protein
- p.Ser923=
- Coding
- c.2769C>T
- MANE Select
- NM_005993
- dbSNP
- rs771565807
- Type
- single nucleotide variant
- Location
- chr17:82929188 (GRCh38)
- Gene constraint
- LOEUF 0.763 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 90.45 · 6 PDB
- Residue 923
- a UniProt-annotated variant site (in)
Similar variants
- TBCD p.Ser923Asn Uncertain significance ★ ⚠ same residue
- TBCD c.1224-2A>G Pathogenic/Likely pathogenic ★★ same type
- TBCD c.2007-2A>G Likely pathogenic ★★ same type
- TBCD p.Ala475Thr Pathogenic/Likely pathogenic ★★ same type
- TBCD p.Ala554Val Pathogenic/Likely pathogenic ★★ same type
- TBCD p.Arg113Ter Pathogenic/Likely pathogenic ★★ same type
- TBCD p.Arg303Ter Pathogenic/Likely pathogenic ★★ same type
- TBCD p.Arg323Ter Pathogenic/Likely pathogenic ★★ 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/tbcd-p-ser923 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown