Is TEK p.Val429fs (c.1284del) pathogenic?

TEK p.Val429fs (c.1284del) is classified Likely pathogenic in TEK (ClinVar, Single submitter, 1 submitter; last evaluated 2025-08-03). Associated with glaucoma 3, primary congenital, E.

What condition is associated with TEK p.Val429fs (c.1284del)?

TEK p.Val429fs (c.1284del) is associated with glaucoma 3, primary congenital, E (ClinVar).

TEK p.Val429fs

c.1284del · VCV4813690

Likely pathogenic Single submitter

Classification

Likely pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Rare

Conditions

glaucoma 3, primary congenital, E

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function in a LoF-intolerant gene
NMD	predicted	premature termination codon in exon 9 of 23
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 7.6	GERP 2, phastCons 1

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Variant & gene context

Gene: TEK
Protein: p.Val429fs
Coding: c.1284del
MANE Select: NM_000459
Type: Deletion
Location: chr9:27185586 (GRCh38)
Gene constraint: LOEUF 0.368 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 84.37 · 17 PDB
Residue 429: the ig-like c2-type 2 domain

Full TEK gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

glaucoma 3, primary congenital, E — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

TEK p.Lys145fs Likely pathogenic ★ same condition
TEK p.Tyr193fs Likely pathogenic ★ same condition
TEK p.Gln518Ter Pathogenic/Likely pathogenic ★★ same condition
TEK p.Leu444fs Likely pathogenic ★★ same condition
TEK p.Arg1076Trp Uncertain significance ★★ ⚠ same condition
TEK c.2209+17A>G Benign ★★ same condition
TEK c.3063-49C>T Benign ★★ same condition
TEK c.761-40C>T Benign ★★ 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-val429fs (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown