TCAP p.Gln56=
c.168G>A · rs1060504769 · VCV416207
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 6.21e-05%)
Conditions
2
hypertrophic cardiomyopathy 25
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 5.2 | GERP 1.5, phastCons 1 |
| Overall | ||
| CADD | 13.07 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
6.21e-05%
Overall
6.21e-05%
1/1,609,906 alleles · very rare
exomes 0/1,457,706 · genomes 1/152,200 · 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.Gln56=
- Coding
- c.168G>A
- MANE Select
- NM_003673
- dbSNP
- rs1060504769
- Type
- single nucleotide variant
- Location
- chr17:39665773 (GRCh38)
- Gene constraint
- LOEUF 1.374 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 79.89 · 2 PDB
Similar variants
- TCAP p.Gln56Ter Pathogenic ★ 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
- TCAP c.*292G>A 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-gln56 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown