Is TAOK2 p.Pro438= (c.1314T>C) pathogenic?

TAOK2 p.Pro438= (c.1314T>C) is classified Likely benign in TAOK2 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-10-18). Absent from gnomAD v4.1.

How common is TAOK2 p.Pro438= (c.1314T>C) in the general population?

TAOK2 p.Pro438= (c.1314T>C) is absent from gnomAD v4.1 (gnomAD).

TAOK2 p.Pro438=

c.1314T>C · rs2543639055 · VCV2769993

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP 0.002	GERP -1.7, phastCons 0.7
Overall
CADD	8.5	PHRED · no single calibrated threshold — expert panels disagree

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: TAOK2
Protein: p.Pro438=
Coding: c.1314T>C
MANE Select: NM_016151
dbSNP: rs2543639055
Type: single nucleotide variant
Location: chr16:29983556 (GRCh38)
Gene constraint: LOEUF 0.459 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 67.17
Residue 438: the 'disordered' region

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

Similar variants

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
TAOK2 p.Ala761Val Uncertain significance ★★ ⚠ same type
TAOK2 p.Ala988Val 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-pro438 (accessed [today's date]).

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