Is TEK p.Glu893Val (c.2678A>T) pathogenic?

TEK p.Glu893Val (c.2678A>T) is classified Likely pathogenic in TEK (ClinVar, Single submitter, 2 submitters; last evaluated 2022-03-08). AlphaMissense: likely pathogenic (0.9467); Absent from gnomAD v4.1; Associated with TEK-related disorder.

What condition is associated with TEK p.Glu893Val (c.2678A>T)?

TEK p.Glu893Val (c.2678A>T) is associated with TEK-related disorder, multiple cutaneous and mucosal venous malformations (ClinVar).

How common is TEK p.Glu893Val (c.2678A>T) in the general population?

TEK p.Glu893Val (c.2678A>T) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about TEK p.Glu893Val (c.2678A>T)?

AlphaMissense predicts likely pathogenic (score 0.9467) — an in-silico prediction, not a clinical call.

TEK p.Glu893Val

c.2678A>T · rs1825511679 · VCV917490

Likely pathogenic Single submitter

Classification

Likely pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 2 submitters

AlphaMissense

likely pathogenic

0.9467 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

2/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

TEK-related disorder

Computational evidence

Protein change
AlphaMissense	0.9467	likely pathogenic ✓ concordant with ClinVar
REVEL	0.801	moderately pathogenic-leaning
SaProt	LLR -8.38	tolerated
⇒ AlphaMissense and REVEL call this damaging; SaProt does not.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 11	GERP 1.8, phastCons 1
Regional constraint	o/e 0.57	unconstrained · MANE · 6,039 bp · p 1.3e-05 · regional, not allelic
Overall
CADD	28.8	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: TEK
Protein: p.Glu893Val
Coding: c.2678A>T
MANE Select: NM_000459
dbSNP: rs1825511679
Type: single nucleotide variant
Location: chr9:27209223 (GRCh38)
Gene constraint: LOEUF 0.368 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 84.37 · 17 PDB
Residue 893: the protein kinase domain; a β-strand

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

Disease context

TEK-related disorder

Also linked: multiple cutaneous and mucosal venous malformations

Similar variants

TEK p.Glu893Gln Uncertain significance ★ ⚠ same residue
TEK p.Arg1099Ter Pathogenic ★★ same condition
TEK p.Arg849Trp Pathogenic ★★ ⚠ same condition
TEK p.Arg915Cys Pathogenic/Likely pathogenic ★★ same condition
TEK p.Arg915His Pathogenic/Likely pathogenic ★★ same condition
TEK p.Arg918Cys Pathogenic/Likely pathogenic ★★ same condition
TEK p.Gln518Ter Pathogenic/Likely pathogenic ★★ same condition
TEK p.Glu1109Ter Pathogenic/Likely pathogenic ★★ 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-glu893val (accessed [today's date]).

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