TCAP p.Glu80=
c.240G>A · rs758101613 · VCV1107933
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00221%, sas)
Conditions
3
Cardiovascular phenotype
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 1.3 | GERP -3.3, phastCons 1 |
| Overall | ||
| CADD | 6.754 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00221%
South Asian · 2/90,666 alleles
Filtering AF
0.000366%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000137%
Overall
0.000186%
3/1,609,812 alleles · very rare
exomes 3/1,457,468 · genomes 0/152,344 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.00221% | 45,333 |
| European (non-Finnish) | 8.48e-05% | 1,178,555 |
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.Glu80=
- Coding
- c.240G>A
- MANE Select
- NM_003673
- dbSNP
- rs758101613
- Type
- single nucleotide variant
- Location
- chr17:39665845 (GRCh38)
- Gene constraint
- LOEUF 1.374 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 79.89 · 2 PDB
- Residue 80
- a β-strand
Similar variants
- TCAP p.Glu80Asp Uncertain significance ★★ ⚠ same residue
- TCAP p.Glu80Gly Uncertain significance ★ ⚠ same residue
- TCAP p.Cys57Ter Pathogenic/Likely pathogenic ★★ same condition
- TCAP p.Gln53Ter Pathogenic/Likely pathogenic ★★ same condition
- TCAP p.Glu35Ter Pathogenic ★★ same condition
- TCAP p.Trp22Ter Pathogenic/Likely pathogenic ★★ same condition
- TCAP p.Trp25Ter Pathogenic/Likely pathogenic ★★ same condition
- TCAP c.110+4A>G Uncertain significance ★★ 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/tcap-p-glu80 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown