TEK p.Thr1106=
c.3318G>C · rs573240128 · VCV744409
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.116%, afr)
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 -1.8 | GERP -3.8 |
| Overall | ||
| CADD | 1.441 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.116%
African / African-American · 87/75,020 alleles
Filtering AF
0.0963%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.089%
Overall
0.00582%
94/1,613,764 alleles · rare
exomes 35/1,461,476 · genomes 59/152,288 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.116% | 862 |
| Remaining individualsnot grpmax-eligible | 0.008% | 12,499 |
| Admixed American | 0.00333% | 30,002 |
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.Thr1106=
- Coding
- c.3318G>C
- MANE Select
- NM_000459
- dbSNP
- rs573240128
- Type
- single nucleotide variant
- Location
- chr9:27229175 (GRCh38)
- Gene constraint
- LOEUF 0.368 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 84.37 · 17 PDB
Similar variants
- TEK p.Thr1106Met 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-thr1106 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown