Is CSNK2B p.Asp64fs (c.192del) pathogenic?

CSNK2B p.Asp64fs (c.192del) is classified Pathogenic in CSNK2B (ClinVar, Single submitter, 1 submitter; last evaluated 2023-09-01). Absent from gnomAD.

How common is CSNK2B p.Asp64fs (c.192del) in the general population?

CSNK2B p.Asp64fs (c.192del) is absent from gnomAD (gnomAD).

CSNK2B p.Asp64fs

c.192del · rs2536962628 · VCV2583035

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

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 4 of 7
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 11	GERP 1.7, 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.Asp64fs
Coding: c.192del
MANE Select: NM_001320
dbSNP: rs2536962628
Type: Deletion
Location: chr6:31668555 (GRCh38)
Gene constraint: LOEUF 0.237 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 93.70 · 10 PDB
Residue 64: 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

Similar variants

CSNK2B p.Asp155fs Pathogenic ★★ same type
CSNK2B p.Phe106fs Pathogenic/Likely pathogenic ★★ same type
CSNK2B c.176-1_176del Pathogenic ★ same type
CSNK2B c.292-2del Pathogenic ★ same type
CSNK2B c.367+5del Likely pathogenic ★ same type
CSNK2B p.Arg178fs Likely pathogenic ★ same type
CSNK2B p.Asp32fs Pathogenic ★ same type
CSNK2B p.Asp70fs Pathogenic ★ same type

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-asp64fs (accessed [today's date]).

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