TEK p.Leu338=
c.1014C>G · VCV4902806
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00893%, eas)
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 -1.1 | GERP -3.5 |
| Overall | ||
| CADD | 1.316 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00893%
East Asian · 4/44,808 alleles
Filtering AF
0.00298%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0018%
Overall
0.000248%
4/1,613,306 alleles · very rare
exomes 3/1,461,192 · genomes 1/152,114 · 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.Leu338=
- Coding
- c.1014C>G
- MANE Select
- NM_000459
- Type
- single nucleotide variant
- Location
- chr9:27180352 (GRCh38)
- Gene constraint
- LOEUF 0.368 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 84.37 · 17 PDB
- Residue 338
- the egf-like 3 domain
Similar variants
- TEK p.Leu338Ile Uncertain significance ★ ⚠ same residue
- TEK p.Arg1099Ter Pathogenic ★★ same type
- TEK p.Arg849Trp Pathogenic ★★ ⚠ same type
- TEK p.Arg915Cys Pathogenic/Likely pathogenic ★★ same type
- TEK p.Arg915His Pathogenic/Likely pathogenic ★★ same type
- TEK p.Arg918Cys Pathogenic/Likely pathogenic ★★ same type
- TEK p.Gln518Ter Pathogenic/Likely pathogenic ★★ same type
- TEK p.Glu1109Ter Pathogenic/Likely pathogenic ★★ same type
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-leu338 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown