Is CHKB p.Gln156fs (c.467_468del) pathogenic?

CHKB p.Gln156fs (c.467468del) is classified Likely pathogenic in CHKB (ClinVar, Single submitter, 1 submitter; last evaluated 2021-04-12). Absent from gnomAD.

How common is CHKB p.Gln156fs (c.467_468del) in the general population?

CHKB p.Gln156fs (c.467_468del) is absent from gnomAD (gnomAD).

CHKB p.Gln156fs

c.467_468del · rs2146656223 · VCV1691030

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

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function
NMD	predicted	premature termination codon in exon 4 of 11
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 7.6	GERP 2.6, 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: CHKB
Protein: p.Gln156fs
Coding: c.467_468del
MANE Select: NM_005198
dbSNP: rs2146656223
Type: Deletion
Location: chr22:50581533 (GRCh38)
Gene constraint: LOEUF 1.015 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 86.54 · 3 PDB
Residue 156: a UniProt-annotated variant site (in mdcmc; loss of choline kinase activity; decreased amount of phosphatidylcholine in patients cells); an α-helix

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

Similar variants

CHKB p.Gln156= Uncertain significance ★ same residue
CHKB p.Phe189fs Pathogenic/Likely pathogenic ★★ same type
CHKB c.582-13_582-11del Benign/Likely benign ★★ same type
CHKB p.Gln198fs Pathogenic ★ same type
CHKB p.Met179fs Pathogenic ★ same type
CHKB p.Thr155fs Pathogenic ★ same type
CHKB c.736+5_736+7del Uncertain significance ★ same type
CHKB c.819-16_819-7del Uncertain significance ★ 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/chkb-p-gln156fs (accessed [today's date]).

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