Is PTK2B p.Val552= (c.1656C>T) pathogenic?

PTK2B p.Val552= (c.1656C>T) is classified Likely benign in PTK2B (ClinVar, Single submitter, 1 submitter; last evaluated 2025-01-01). Absent from gnomAD v4.1.

How common is PTK2B p.Val552= (c.1656C>T) in the general population?

PTK2B p.Val552= (c.1656C>T) is absent from gnomAD v4.1 (gnomAD).

PTK2B p.Val552=

c.1656C>T · VCV3772216

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	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -0.35	GERP -2.8, phastCons 0.089
Overall
CADD	7.229	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: PTK2B
Protein: p.Val552=
Coding: c.1656C>T
MANE Select: NM_173176
Type: single nucleotide variant
Location: chr8:27439043 (GRCh38)
Gene constraint: LOEUF 0.562 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 76.47 · 26 PDB
Residue 552: the protein kinase domain; an α-helix

Full PTK2B gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

PTK2B p.Gln359Glu Likely benign ★★ same type
PTK2B p.Leu178= Benign ★★ same type
PTK2B p.Pro413= Benign ★★ same type
PTK2B p.Thr264Asn Likely benign ★★ same type
PTK2B p.Ala258Thr Uncertain significance ★ ⚠ same type
PTK2B p.Ala345Thr Uncertain significance ★ ⚠ same type
PTK2B p.Ala709Val Uncertain significance ★ ⚠ same type
PTK2B p.Ala799Val 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/ptk2b-p-val552 (accessed [today's date]).

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