Is TEK p.Pro71= (c.213G>A) pathogenic?

TEK p.Pro71= (c.213G>A) is classified Likely benign in TEK (ClinVar, No assertion criteria, 1 submitter; last evaluated 2019-11-25). Ultra-rare (popmax 0.0329%, mid); Associated with TEK-related disorder.

What condition is associated with TEK p.Pro71= (c.213G>A)?

TEK p.Pro71= (c.213G>A) is associated with TEK-related disorder (ClinVar).

How common is TEK p.Pro71= (c.213G>A) in the general population?

TEK p.Pro71= (c.213G>A) is ultra-rare (popmax 0.0329%, mid) (gnomAD).

TEK p.Pro71=

c.213G>A · rs774440968 · VCV3049125

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0329%, mid)

Conditions

TEK-related disorder

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 -0.3	GERP -3.8
Overall
CADD	9.11	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0329% Middle Eastern · 2/6,084 alleles

Filtering AF 0.0058% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00241%

Overall 0.000805% 13/1,613,912 alleles · ultra-rare

Ancestry group	Frequency	1 in
Middle Easterngrpmax	0.0329%	3,042
South Asian	0.00329%	30,354
East Asian	0.00223%	44,880
European (non-Finnish)	0.000593%	168,574

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.Pro71=
Coding: c.213G>A
MANE Select: NM_000459
dbSNP: rs774440968
Type: single nucleotide variant
Location: chr9:27157991 (GRCh38)
Gene constraint: LOEUF 0.368 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 84.37 · 17 PDB
Residue 71: a disulfide bond; a UniProt-annotated variant site (in glc3e; formation of protein aggregates); the ig-like c2-type 1 domain; an α-helix

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

Disease context

TEK-related disorder

Similar variants

TEK p.Arg849Trp Pathogenic ★★ ⚠ same condition
TEK p.Glu1109Ter Pathogenic/Likely pathogenic ★★ same condition
TEK p.Arg107Ter Likely pathogenic ★ same condition
TEK p.Cys1040Arg Likely pathogenic ★ ⚠ same condition
TEK p.Glu893Val Likely pathogenic ★ ⚠ same condition
TEK p.Thr1037Lys Likely pathogenic ★ ⚠ same condition
TEK p.Pro447Leu Uncertain significance ★ ⚠ same condition
TEK p.Thr1037Ile Conflicting classifications of pathogenicity ★ ⚠ 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-pro71 (accessed [today's date]).

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