Is CSNK2B p.Phe106fs (c.317_318del) pathogenic?

CSNK2B p.Phe106fs (c.317318del) is classified Pathogenic/Likely pathogenic in CSNK2B (ClinVar, Multiple submitters, 3 submitters; last evaluated 2025-10-13). Associated with Poirier-Bienvenu neurodevelopmental syndrome.

What condition is associated with CSNK2B p.Phe106fs (c.317_318del)?

CSNK2B p.Phe106fs (c.317_318del) is associated with Poirier-Bienvenu neurodevelopmental syndrome (ClinVar).

CSNK2B p.Phe106fs

c.317_318del · VCV4852804

Pathogenic/Likely pathogenic Multiple submitters

Classification

Pathogenic/Likely pathogenic

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

Consequence

frameshift

predicted LoF

gnomAD v4.1

Rare

Conditions

Poirier-Bienvenu neurodevelopmental syndrome

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function in a LoF-intolerant gene
NMD	predicted	premature termination codon in exon 5 of 7
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 0.12	GERP -0.51, phastCons 0.92

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Variant & gene context

Gene: CSNK2B
Protein: p.Phe106fs
Coding: c.317_318del
MANE Select: NM_001320
Type: Deletion
Location: chr6:31669121 (GRCh38)
Gene constraint: LOEUF 0.237 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 93.70 · 10 PDB
Residue 106: a UniProt-annotated variant site (in pobinds; associated in cis with c-86); a turn

Full CSNK2B gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Poirier-Bienvenu neurodevelopmental syndrome — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

CSNK2B c.292-2del Pathogenic ★ same condition
CSNK2B c.367+5del Likely pathogenic ★ same condition
CSNK2B p.Arg178fs Likely pathogenic ★ same condition
CSNK2B p.Asp70fs Pathogenic ★ same condition
CSNK2B p.Cys137fs Likely pathogenic ★ same condition
CSNK2B p.Phe163fs Likely pathogenic ★ same condition
CSNK2B p.Phe183fs Likely pathogenic ★ same condition
CSNK2B p.Thr161fs Pathogenic ★ 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/csnk2b-p-phe106fs (accessed [today's date]).

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