TEK p.Pro1038=
c.3114C>G · rs145261015 · VCV2068190
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0441%, 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 -2.7 | GERP -1.1 |
| Overall | ||
| CADD | 6.754 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0441%
African / African-American · 33/74,898 alleles
Filtering AF
0.0322%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0281%
Overall
0.00304%
49/1,613,938 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0441% | 2,270 |
| Middle Eastern | 0.0165% | 6,060 |
| Admixed American | 0.00833% | 12,001 |
| South Asian | 0.00549% | 18,217 |
| Remaining individualsnot grpmax-eligible | 0.0048% | 20,825 |
| European (non-Finnish) | 0.000169% | 589,981 |
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.Pro1038=
- Coding
- c.3114C>G
- MANE Select
- NM_000459
- dbSNP
- rs145261015
- Type
- single nucleotide variant
- Location
- chr9:27220059 (GRCh38)
- Gene constraint
- LOEUF 0.368 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 84.37 · 17 PDB
- Residue 1038
- the protein kinase domain; a turn
Similar variants
- TEK p.Pro1038Ala 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-pro1038 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown