Is TAOK2 p.Arg78= (c.234G>T) pathogenic?

TAOK2 p.Arg78= (c.234G>T) is classified Likely benign in TAOK2 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-03-24). Very rare (popmax 0.00167%, amr).

How common is TAOK2 p.Arg78= (c.234G>T) in the general population?

TAOK2 p.Arg78= (c.234G>T) is very rare (popmax 0.00167%, amr) (gnomAD).

TAOK2 p.Arg78=

c.234G>T · VCV4769790

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00167%, amr)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal.
Splicing
SpliceAI	Δ0.41	donor gain · deltas
Constraint at this position
Conservation	phyloP 0.62	GERP -0.53, phastCons 1
Overall
CADD	16.6	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00167% Admixed American · 1/60,028 alleles

Overall 6.2e-05% 1/1,614,140 alleles · very rare exomes 1/1,461,886 · genomes 0/152,254 · joint denominator

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: TAOK2
Protein: p.Arg78=
Coding: c.234G>T
MANE Select: NM_016151
Type: single nucleotide variant
Location: chr16:29978281 (GRCh38)
Gene constraint: LOEUF 0.459 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 67.17
Residue 78: the protein kinase domain

Full TAOK2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

TAOK2 p.Arg78Gln Uncertain significance ★ ⚠ same residue
TAOK2 p.Arg78Leu Uncertain significance ★ ⚠ same residue
TAOK2 p.Ala1057Val Uncertain significance ★★ ⚠ same type
TAOK2 p.Ala1062Val Uncertain significance ★★ ⚠ same type
TAOK2 p.Ala1148Thr Uncertain significance ★★ ⚠ same type
TAOK2 p.Ala444Val Uncertain significance ★★ ⚠ same type
TAOK2 p.Ala733Val Uncertain significance ★★ ⚠ same type
TAOK2 p.Ala747Val Uncertain significance ★★ ⚠ 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/taok2-p-arg78 (accessed [today's date]).

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