TEK p.Asn680=
c.2040T>C · rs1251094590 · VCV914781
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.0011%, sas)
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 -0.29 | GERP -1.1, phastCons 0.45 |
| Overall | ||
| CADD | 6.349 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0011%
South Asian · 1/91,086 alleles
Overall
6.2e-05%
1/1,614,158 alleles · very rare
exomes 1/1,461,826 · genomes 0/152,332 · 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
- TEK
- Protein
- p.Asn680=
- Coding
- c.2040T>C
- MANE Select
- NM_000459
- dbSNP
- rs1251094590
- Type
- single nucleotide variant
- Location
- chr9:27202950 (GRCh38)
- Gene constraint
- LOEUF 0.368 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 84.37 · 17 PDB
- Residue 680
- the fibronectin type-iii 3 domain
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-p-asn680 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown