Is CSNK2B p.Asp155fs (c.464_467del) pathogenic?

CSNK2B p.Asp155fs (c.464467del) is classified Pathogenic in CSNK2B (ClinVar, Multiple submitters, 2 submitters; last evaluated 2024-05-17). Absent from gnomAD; Associated with Inborn genetic diseases.

What condition is associated with CSNK2B p.Asp155fs (c.464_467del)?

CSNK2B p.Asp155fs (c.464_467del) is associated with Inborn genetic diseases (ClinVar).

How common is CSNK2B p.Asp155fs (c.464_467del) in the general population?

CSNK2B p.Asp155fs (c.464_467del) is absent from gnomAD (gnomAD).

CSNK2B p.Asp155fs

c.464_467del · rs2536968042 · VCV2285081

Pathogenic Multiple submitters

Classification

Pathogenic

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

Inborn genetic diseases

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 6 of 7
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 4.9	GERP -0.85, 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.Asp155fs
Coding: c.464_467del
MANE Select: NM_001320
dbSNP: rs2536968042
Type: Deletion
Location: chr6:31669413 (GRCh38)
Gene constraint: LOEUF 0.237 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 93.70 · 10 PDB
Residue 155: a UniProt-annotated variant site (in pobinds; associated in cis with c-86); a β-strand

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

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

CSNK2B p.Asp155His Uncertain significance ★ ⚠ same residue
CSNK2B p.Asp26Gly Likely pathogenic ★★ same condition
CSNK2B p.Asp32Asn Pathogenic/Likely pathogenic ★★ same condition
CSNK2B p.Gln42Ter Pathogenic ★★ same condition
CSNK2B p.Leu36Pro Pathogenic ★★ same condition
CSNK2B p.Ser149Ter Pathogenic/Likely pathogenic ★★ same condition
CSNK2B c.367+3_367+5delinsAAA Likely pathogenic ★ same condition
CSNK2B p.Gly189Val Likely 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-asp155fs (accessed [today's date]).

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