Is CSNK2B p.Pro179fs (c.533_534insGT) pathogenic?

CSNK2B p.Pro179fs (c.533534insGT) is classified Pathogenic in CSNK2B (ClinVar, No assertion criteria, 1 submitter; last evaluated 2020-03-18). Absent from gnomAD; Associated with Poirier-Bienvenu neurodevelopmental syndrome.

What condition is associated with CSNK2B p.Pro179fs (c.533_534insGT)?

CSNK2B p.Pro179fs (c.533_534insGT) is associated with Poirier-Bienvenu neurodevelopmental syndrome (ClinVar).

How common is CSNK2B p.Pro179fs (c.533_534insGT) in the general population?

CSNK2B p.Pro179fs (c.533_534insGT) is absent from gnomAD (gnomAD).

CSNK2B p.Pro179fs

c.533_534insGT · rs1583611843 · VCV805770

Pathogenic No assertion criteria

Classification

Pathogenic

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

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, 24 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 12	GERP 2.4, phastCons 1

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

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: CSNK2B
Protein: p.Pro179fs
Coding: c.533_534insGT
MANE Select: NM_001320
dbSNP: rs1583611843
Type: Insertion
Location: chr6:31669484 (GRCh38)
Gene constraint: LOEUF 0.237 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 93.70 · 10 PDB
Residue 179: a UniProt-annotated variant site (in pobinds; associated in cis with c-86); an α-helix

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.Glu115fs Pathogenic ★ same condition
CSNK2B c.175+1G>A Pathogenic/Likely pathogenic ★★ same condition
CSNK2B c.291+1G>A Pathogenic/Likely pathogenic ★★ same condition
CSNK2B c.291+1G>T Likely pathogenic ★★ same condition
CSNK2B c.292-2A>C Pathogenic/Likely pathogenic ★★ same condition
CSNK2B c.292-2A>G Pathogenic/Likely pathogenic ★★ same condition
CSNK2B c.557+1G>C Pathogenic/Likely pathogenic ★★ same condition
CSNK2B c.558-2A>G 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-pro179fs (accessed [today's date]).

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