Is CSNK2B p.Phe183fs (c.549del) pathogenic?

CSNK2B p.Phe183fs (c.549del) is classified Likely pathogenic in CSNK2B (ClinVar, Single submitter, 1 submitter; last evaluated 2024-09-13). Associated with Poirier-Bienvenu neurodevelopmental syndrome.

What condition is associated with CSNK2B p.Phe183fs (c.549del)?

CSNK2B p.Phe183fs (c.549del) is associated with Poirier-Bienvenu neurodevelopmental syndrome (ClinVar).

CSNK2B p.Phe183fs

c.549del · VCV4293989

Likely pathogenic Single submitter

Classification

Likely pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

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	escapes	premature termination codon within the last 50 nt of the penultimate exon (6 of 7, 10 nt from its 3' end) — the truncated protein is likely expressed. PVS1 input, not an applied code
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 5.2	GERP 2.4, phastCons 1

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

Variant & gene context

Gene: CSNK2B
Protein: p.Phe183fs
Coding: c.549del
MANE Select: NM_001320
Type: Deletion
Location: chr6:31669498 (GRCh38)
Gene constraint: LOEUF 0.237 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 93.70 · 10 PDB
Residue 183: a UniProt-annotated variant site (in pobinds; associated in cis with c-86)

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 p.Phe106fs Pathogenic/Likely pathogenic ★★ same condition
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.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-phe183fs (accessed [today's date]).

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