Is CSNK2B p.Phe34fs (c.99dup) pathogenic?

CSNK2B p.Phe34fs (c.99dup) is classified Likely pathogenic in CSNK2B (ClinVar, Single submitter, 1 submitter; last evaluated 2022-07-14). Absent from gnomAD; Associated with Poirier-Bienvenu neurodevelopmental syndrome.

What condition is associated with CSNK2B p.Phe34fs (c.99dup)?

CSNK2B p.Phe34fs (c.99dup) is associated with Poirier-Bienvenu neurodevelopmental syndrome (ClinVar).

How common is CSNK2B p.Phe34fs (c.99dup) in the general population?

CSNK2B p.Phe34fs (c.99dup) is absent from gnomAD (gnomAD).

CSNK2B p.Phe34fs

c.99dup · rs2536957939 · VCV1709608

Likely pathogenic Single submitter

Classification

Likely pathogenic

ClinVar

Review

Single submitter ★☆☆☆

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	predicted	premature termination codon in exon 3 of 7
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 1.4	GERP -0.52, 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.Phe34fs
Coding: c.99dup
MANE Select: NM_001320
dbSNP: rs2536957939
Type: Duplication
Location: chr6:31667891 (GRCh38)
Gene constraint: LOEUF 0.237 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 93.70 · 10 PDB
Residue 34: 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.Ala196fs Likely pathogenic ★ same condition
CSNK2B p.Arg186fs Likely pathogenic ★ same condition
CSNK2B p.Gln198fs Likely pathogenic ★ same condition
CSNK2B p.Phe34Cys Likely pathogenic ★ same residue
CSNK2B p.Thr90fs Pathogenic ★ same condition
CSNK2B p.Phe34Leu Uncertain significance ★ ⚠ same residue
CSNK2B p.Lys139fs Pathogenic same condition
CSNK2B p.Lys208fs 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-phe34fs (accessed [today's date]).

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