TEK c.*287C>T
Uncertain significance
Multiple submitters
Classification
Uncertain significance
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.318%, mid)
Conditions
1
multiple cutaneous and mucosal venous malformations
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 | GERP -3.5, phastCons 0.99 |
| Non-coding constraint | Z -4.04 | 1 kb window · o/e 1.29 · regional · uncalibrated |
| Overall | ||
| CADD | 7.052 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.318%
Middle Eastern · 5/1,570 alleles
Filtering AF
0.125%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0977%
Overall
0.0336%
148/440,600 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.318% | 314 |
| Admixed American | 0.145% | 692 |
| European (non-Finnish) | 0.033% | 3,030 |
| South Asian | 0.0325% | 3,080 |
| Finnishnot grpmax-eligible | 0.0118% | 8,446 |
| Remaining individualsnot grpmax-eligible | 0.0107% | 9,349 |
| African / African-American | 0.00794% | 12,591 |
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
- TEK
- Coding
- c.*287C>T
- MANE Select
- NM_000459
- dbSNP
- rs562001960
- Type
- single nucleotide variant
- Location
- chr9:27229519 (GRCh38)
- Gene constraint
- LOEUF 0.368 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 84.37 · 17 PDB
Similar variants
- TEK p.Arg1099Ter Pathogenic ★★ same condition
- TEK p.Arg849Trp Pathogenic ★★ ⚠ same condition
- TEK p.Arg915Cys Pathogenic/Likely pathogenic ★★ same condition
- TEK p.Arg915His Pathogenic/Likely pathogenic ★★ same condition
- TEK p.Arg918Cys Pathogenic/Likely pathogenic ★★ same condition
- TEK p.Gln518Ter Pathogenic/Likely pathogenic ★★ same condition
- TEK p.Tyr897Asn Pathogenic/Likely pathogenic ★★ ⚠ same condition
- TEK p.Tyr897Cys 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/tek-c-star-287c-t (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown