Is TAOK2 p.Ala522= (c.1566A>C) pathogenic?

TAOK2 p.Ala522= (c.1566A>C) is classified Likely benign in TAOK2 (ClinVar, Single submitter, 1 submitter; last evaluated 2026-01-04). Very rare (popmax 0.00267%, afr).

How common is TAOK2 p.Ala522= (c.1566A>C) in the general population?

TAOK2 p.Ala522= (c.1566A>C) is very rare (popmax 0.00267%, afr) (gnomAD).

TAOK2 p.Ala522=

c.1566A>C · rs967071705 · VCV2168681

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00267%, 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 -3	GERP -3.8
Overall
CADD	1.254	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00267% African / African-American · 2/74,894 alleles

Filtering AF 0.000443% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000166%

Overall 0.000496% 8/1,611,664 alleles · very rare exomes 5/1,459,450 · genomes 3/152,214 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.00267%	37,447
European (non-Finnish)	0.000509%	196,457

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.Ala522=
Coding: c.1566A>C
MANE Select: NM_016151
dbSNP: rs967071705
Type: single nucleotide variant
Location: chr16:29985356 (GRCh38)
Gene constraint: LOEUF 0.459 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 67.17

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

Similar variants

TAOK2 p.Ala522Thr Uncertain significance ★ ⚠ same residue
TAOK2 p.Ala522Val 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-ala522 (accessed [today's date]).

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