Is CLPB p.Pro670fs (c.2009_2010del) pathogenic?

CLPB p.Pro670fs (c.20092010del) is classified Uncertain significance in CLPB (ClinVar, Single submitter, 1 submitter; last evaluated 2022-10-27). Very rare (popmax 0.00133%, afr); Associated with 3-methylglutaconic aciduria, type VIIB.

What condition is associated with CLPB p.Pro670fs (c.2009_2010del)?

CLPB p.Pro670fs (c.2009_2010del) is associated with 3-methylglutaconic aciduria, type VIIB (ClinVar).

How common is CLPB p.Pro670fs (c.2009_2010del) in the general population?

CLPB p.Pro670fs (c.2009_2010del) is very rare (popmax 0.00133%, afr) (gnomAD).

CLPB p.Pro670fs

Q: How is 3-methylglutaconic aciduria-neonatal cataract-neurologic involvement-congenital neutropenia syndrome inherited?

Typically Autosomal recessive (Orphanet). A genetic counselor can assess individual risk for a family.

c.2009_2010del · rs2539312407 · VCV2809996

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Rare

very rare (popmax 0.00133%, afr)

Conditions

3-methylglutaconic aciduria, type VIIB

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function
NMD	escapes	premature termination codon in the last exon (16 of 16) — the truncated protein is likely expressed. PVS1 input, not an applied code
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 4.9	GERP 1.8, phastCons 1

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00133% African / African-American · 1/75,048 alleles

Overall 6.2e-05% 1/1,614,062 alleles · very rare exomes 1/1,461,774 · genomes 0/152,288 · joint denominator

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: CLPB
Protein: p.Pro670fs
Coding: c.2009_2010del
MANE Select: NM_001258392
dbSNP: rs2539312407
Type: Deletion
Location: chr11:72293391 (GRCh38)
Gene constraint: LOEUF 0.643 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 72.52 · 7 PDB

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

Disease context

3-methylglutaconic aciduria, type VIIB — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For 3-methylglutaconic aciduria-neonatal cataract-neurologic involvement-congenital neutropenia syndrome (Orphanet):

Inheritance: Autosomal recessive
Onset: Antenatal, Neonatal

Similar variants

CLPB p.Asn675fs Uncertain significance ★★ same condition
CLPB c.1561-18_1561-12del Likely benign ★★ same condition
CLPB c.403+7_403+8del Likely benign ★★ same condition
CLPB c.543-20_543-18del Likely benign ★★ same condition
CLPB c.1560+2_1560+5del Likely pathogenic ★ same condition
CLPB p.Asp448fs Pathogenic ★ same condition
CLPB p.Leu263fs Pathogenic ★ same condition
CLPB p.Val107fs 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/clpb-p-pro670fs (accessed [today's date]).

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