Is CPT1C p.Ser178= (c.534T>C) pathogenic?

CPT1C p.Ser178= (c.534T>C) is classified Likely benign in CPT1C (ClinVar, Single submitter, 1 submitter; last evaluated 2022-08-01). Absent from gnomAD v4.1.

How common is CPT1C p.Ser178= (c.534T>C) in the general population?

CPT1C p.Ser178= (c.534T>C) is absent from gnomAD v4.1 (gnomAD).

CPT1C p.Ser178=

c.534T>C · rs769339964 · VCV2650284

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -6.8
Overall
CADD	2.298	PHRED · no single calibrated threshold — expert panels disagree

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.Ser178=
Coding: c.534T>C
MANE Select: NM_001199753
dbSNP: rs769339964
Type: single nucleotide variant
Location: chr19:49701397 (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 p.Ser178Pro Uncertain significance ★ ⚠ same residue
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

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-ser178 (accessed [today's date]).

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