TCAP p.Leu40=
c.118C>T · rs886043427 · VCV286576
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00335%, amr)
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 0.62 | GERP -0.7, phastCons 0.21 |
| Overall | ||
| CADD | 7.793 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00335%
Admixed American · 2/59,718 alleles
Filtering AF
0.000556%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000208%
Overall
0.000124%
2/1,610,210 alleles · very rare
exomes 2/1,457,914 · genomes 0/152,296 · joint denominator
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
- TCAP
- Protein
- p.Leu40=
- Coding
- c.118C>T
- MANE Select
- NM_003673
- dbSNP
- rs886043427
- Type
- single nucleotide variant
- Location
- chr17:39665723 (GRCh38)
- Gene constraint
- LOEUF 1.374 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 79.89 · 2 PDB
- Residue 40
- a β-strand
Similar variants
- TCAP c.110+5G>T Likely pathogenic ★★ same type
- TCAP p.Cys57Ter Pathogenic/Likely pathogenic ★★ same type
- TCAP p.Gln53Ter Pathogenic/Likely pathogenic ★★ same type
- TCAP p.Glu35Ter Pathogenic ★★ same type
- TCAP p.Trp22Ter Pathogenic/Likely pathogenic ★★ same type
- TCAP p.Trp25Ter Pathogenic/Likely pathogenic ★★ same type
- TCAP c.110+4A>G Uncertain significance ★★ same type
- TCAP c.*292G>A 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/tcap-p-leu40 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown