Is CLPP p.Ile132Thr (c.395T>C) pathogenic?

CLPP p.Ile132Thr (c.395T>C) is classified Uncertain significance in CLPP (ClinVar, Single submitter, 1 submitter; last evaluated 2024-07-01). AlphaMissense: likely pathogenic (0.9873); Absent from gnomAD v4.1.

How common is CLPP p.Ile132Thr (c.395T>C) in the general population?

CLPP p.Ile132Thr (c.395T>C) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about CLPP p.Ile132Thr (c.395T>C)?

AlphaMissense predicts likely pathogenic (score 0.9873) — an in-silico prediction, not a clinical call.

CLPP p.Ile132Thr

c.395T>C · VCV3257209

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.9873 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

3/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.9873	likely pathogenic
REVEL	0.938	strongly pathogenic-leaning
SaProt	LLR -14.10	damaging
⇒ AlphaMissense, REVEL and SaProt all call this damaging.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 7.8	GERP 2.1, phastCons 1
Regional constraint	o/e 0.76	unconstrained · MANE · 6,803 bp · p 5e-05 · regional, not allelic
Overall
CADD	29.2	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean damaging — a triage signal, not a reclassification

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

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: CLPP
Protein: p.Ile132Thr
Coding: c.395T>C
MANE Select: NM_006012
Type: single nucleotide variant
Location: chr19:6364479 (GRCh38)
Gene constraint: LOEUF 0.936 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 82.68 · 32 PDB
Residue 132: an α-helix

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

Similar variants

CLPP c.368-2A>G Pathogenic/Likely pathogenic ★★ same type
CLPP p.Ala10Gly Uncertain significance ★★ ⚠ same type
CLPP p.Ala10Ser Uncertain significance ★★ ⚠ same type
CLPP p.Ala128Thr Uncertain significance ★★ ⚠ same type
CLPP p.Ala223Thr Uncertain significance ★★ ⚠ same type
CLPP p.Ala43Thr Uncertain significance ★★ ⚠ same type
CLPP p.Ala50Thr Uncertain significance ★★ ⚠ same type
CLPP p.Arg174Cys 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/clpp-p-ile132thr (accessed [today's date]).

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