Is CLPB p.Val150fs (c.449_455del) pathogenic?

CLPB p.Val150fs (c.449455del) is classified Pathogenic in CLPB (ClinVar, Single submitter, 1 submitter). Absent from gnomAD; Associated with neutropenia, severe congenital, 9, autosomal dominant.

What condition is associated with CLPB p.Val150fs (c.449_455del)?

CLPB p.Val150fs (c.449_455del) is associated with neutropenia, severe congenital, 9, autosomal dominant (ClinVar).

How common is CLPB p.Val150fs (c.449_455del) in the general population?

CLPB p.Val150fs (c.449_455del) is absent from gnomAD (gnomAD).

CLPB p.Val150fs

c.449_455del · rs2495982812 · VCV2506998

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

Conditions

neutropenia, severe congenital, 9, autosomal dominant

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 2 of 16
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 7.7	GERP 1.6, 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: CLPB
Protein: p.Val150fs
Coding: c.449_455del
MANE Select: NM_001258392
dbSNP: rs2495982812
Type: Deletion
Location: chr11:72430312 (GRCh38)
Gene constraint: LOEUF 0.643 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 72.52 · 7 PDB
Residue 150: an α-helix

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

Disease context

neutropenia, severe congenital, 9, autosomal dominant — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

CLPB p.Val150= Likely benign ★ same residue
CLPB p.Arg378Gly Pathogenic/Likely pathogenic ★★ same condition
CLPB p.Arg387Ter Pathogenic ★★ same condition
CLPB p.Arg143His Uncertain significance ★★ ⚠ same condition
CLPB p.Arg250Gly Uncertain significance ★★ ⚠ same condition
CLPB p.Arg599Cys Uncertain significance ★★ ⚠ same condition
CLPB p.Gly218Ala Uncertain significance ★★ ⚠ same condition
CLPB p.Met282Val Uncertain significance ★★ ⚠ 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/clpb-p-val150fs (accessed [today's date]).

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