Is CPT1C p.Ala142Val (c.425C>T) pathogenic?

CPT1C p.Ala142Val (c.425C>T) is classified Uncertain significance in CPT1C (ClinVar, Single submitter, 1 submitter; last evaluated 2025-08-28). AlphaMissense: likely benign (0.0762); Absent from gnomAD v4.1.

How common is CPT1C p.Ala142Val (c.425C>T) in the general population?

CPT1C p.Ala142Val (c.425C>T) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about CPT1C p.Ala142Val (c.425C>T)?

AlphaMissense predicts likely benign (score 0.0762) — an in-silico prediction, not a clinical call.

CPT1C p.Ala142Val

c.425C>T · VCV4233614

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0762 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.0762	likely benign
REVEL	0.191	benign-leaning
SaProt	LLR -6.56	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	<0.2	all four deltas below 0.2 · C>G here scores Δ0.74 · evaluated, not missing
Constraint at this position
Conservation	phyloP 0.75	phastCons 0.2
Regional constraint	o/e 0.99	unconstrained · MANE · 15 kb · p 0.77 · regional, not allelic
Overall
CADD	19.8	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — 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: CPT1C
Protein: p.Ala142Val
Coding: c.425C>T
MANE Select: NM_001199753
Type: single nucleotide variant
Location: chr19:49700827 (GRCh38)
Gene constraint: LOEUF 0.778 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 88.81 · 1 PDB

Full CPT1C gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CPT1C c.1160+3A>G Uncertain significance ★★ same type
CPT1C p.Ala117Val Uncertain significance ★★ ⚠ same type
CPT1C p.Ala19Thr Uncertain significance ★★ ⚠ same type
CPT1C p.Ala203Thr Uncertain significance ★★ ⚠ same type
CPT1C p.Ala401Val Uncertain significance ★★ ⚠ same type
CPT1C p.Ala422Thr Uncertain significance ★★ ⚠ same type
CPT1C p.Ala431Val Uncertain significance ★★ ⚠ same type
CPT1C p.Ala4Glu 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/cpt1c-p-ala142val (accessed [today's date]).

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