TEK p.Thr250=
c.750G>A · rs76324455 · VCV778425
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.33%, 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 -2.6 | GERP -3.2 |
| Overall | ||
| CADD | 1.835 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.33%
African / African-American · 1,001/74,992 alleles
Filtering AF
1.27%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.24%
Overall
0.0749%
1,209/1,613,548 alleles · low-frequency
exomes 621/1,461,252 · genomes 588/152,296 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.33% | 75 |
| Admixed American | 0.105% | 952 |
| Remaining individualsnot grpmax-eligible | 0.102% | 976 |
| South Asian | 0.0637% | 1,570 |
| Middle Eastern | 0.0495% | 2,020 |
| European (non-Finnish) | 0.0017% | 58,980 |
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.Thr250=
- Coding
- c.750G>A
- MANE Select
- NM_000459
- dbSNP
- rs76324455
- Type
- single nucleotide variant
- Location
- chr9:27172737 (GRCh38)
- Gene constraint
- LOEUF 0.368 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 84.37 · 17 PDB
- Residue 250
- the egf-like 1 domain
Similar variants
- 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
- TEK p.Tyr897Asn 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-thr250 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown