TEK p.Asn560=
c.1680T>C · rs35357088 · VCV366427
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 7 submitters
gnomAD v4.1
Common
common (popmax 23.3%, amr) — too common for a highly-penetrant pathogenic allele
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 2.7 | GERP -0.6, phastCons 1 |
| Overall | ||
| CADD | 8.833 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
23.3%
Admixed American · 14,002/60,008 alleles
Filtering AF
23%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 22.9%
Overall
6.65%
107,403/1,614,038 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 23.3% | 4 |
| Finnishnot grpmax-eligible | 13.3% | 8 |
| European (non-Finnish) | 6.44% | 16 |
| Remaining individualsnot grpmax-eligible | 5.53% | 18 |
| Ashkenazi Jewishnot grpmax-eligible | 3.69% | 27 |
| South Asian | 3.45% | 29 |
| Amishnot grpmax-eligible | 2.52% | 40 |
| Middle Eastern | 2.34% | 43 |
| African / African-American | 1.27% | 79 |
| East Asian | 0.0824% | 1,213 |
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.Asn560=
- Coding
- c.1680T>C
- MANE Select
- NM_000459
- dbSNP
- rs35357088
- Type
- single nucleotide variant
- Location
- chr9:27197370 (GRCh38)
- Gene constraint
- LOEUF 0.368 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 84.37 · 17 PDB
- Residue 560
- the fibronectin type-iii 2 domain; a β-strand
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-asn560 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown