Is CLPB p.Asn418Ser (c.1253A>G) pathogenic?

CLPB p.Asn418Ser (c.1253A>G) is classified Conflicting classifications of pathogenicity in CLPB (ClinVar, Conflicting submitters, 5 submitters; last evaluated 2026-01-30). AlphaMissense: likely benign (0.0685); Rare (popmax 0.376%, afr); Associated with 3-methylglutaconic aciduria, type VIIB.

What condition is associated with CLPB p.Asn418Ser (c.1253A>G)?

CLPB p.Asn418Ser (c.1253A>G) is associated with 3-methylglutaconic aciduria, type VIIB (ClinVar).

How common is CLPB p.Asn418Ser (c.1253A>G) in the general population?

CLPB p.Asn418Ser (c.1253A>G) is rare (popmax 0.376%, afr) (gnomAD).

What do computational predictors say about CLPB p.Asn418Ser (c.1253A>G)?

AlphaMissense predicts likely benign (score 0.0685) — an in-silico prediction, not a clinical call.

CLPB p.Asn418Ser

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.1253A>G · rs116118397 · VCV476192

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 5 submitters

AlphaMissense

likely benign

0.0685 · ACMG-weighted

gnomAD v4.1

Rare

rare (popmax 0.376%, afr)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

3-methylglutaconic aciduria, type VIIB

Computational evidence

Protein change
AlphaMissense	0.0685	likely benign
REVEL	0.125	moderately benign-leaning
SaProt	LLR -6.06	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 7.9	GERP 1.6, phastCons 1
Regional constraint	o/e 0.54	unconstrained · MANE · 22 kb · p 2.6e-09 · regional, not allelic
Overall
CADD	22.7	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

⚠ Isoform check: AlphaMissense numbered on a different transcript (AM N448S vs ClinVar N418S) — verify the residue.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.376% African / African-American · 282/75,050 alleles

Filtering AF 0.34% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.326%

Overall 0.0236% 381/1,614,164 alleles · rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.376%	266
Middle Eastern	0.033%	3,031
Remaining individualsnot grpmax-eligible	0.0288%	3,473
Admixed American	0.0233%	4,288
South Asian	0.0176%	5,692
East Asian	0.00891%	11,220
European (non-Finnish)	0.00381%	26,222

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.Asn418Ser
Coding: c.1253A>G
MANE Select: NM_001258392
dbSNP: rs116118397
Type: single nucleotide variant
Location: chr11:72301879 (GRCh38)
Gene constraint: LOEUF 0.643 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 72.52 · 7 PDB
Residue 418: an α-helix

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.Asn418His Uncertain significance ★ ⚠ same residue
CLPB c.1066+1G>A Pathogenic/Likely pathogenic ★★ same condition
CLPB c.455+1G>A Likely pathogenic ★★ same condition
CLPB c.873+1G>A Pathogenic/Likely pathogenic ★★ same condition
CLPB c.874-2A>G Likely pathogenic ★★ same condition
CLPB p.Arg178Ter Pathogenic ★★ same condition
CLPB p.Arg312Ter Pathogenic/Likely pathogenic ★★ same condition
CLPB p.Arg378Gly Pathogenic/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/clpb-p-asn418ser (accessed [today's date]).

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