Is CPT1C p.Met798Val (c.2392A>G) pathogenic?

CPT1C p.Met798Val (c.2392A>G) is classified Benign/Likely benign in CPT1C (ClinVar, Multiple submitters, 4 submitters; last evaluated 2026-01-15). AlphaMissense: likely benign (0.054); Rare (popmax 0.41%, nfe); Associated with hereditary spastic paraplegia 73.

What condition is associated with CPT1C p.Met798Val (c.2392A>G)?

CPT1C p.Met798Val (c.2392A>G) is associated with hereditary spastic paraplegia 73 (ClinVar).

How common is CPT1C p.Met798Val (c.2392A>G) in the general population?

CPT1C p.Met798Val (c.2392A>G) is rare (popmax 0.41%, nfe) (gnomAD).

How is Autosomal dominant spastic paraplegia type 73 inherited?

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

What do computational predictors say about CPT1C p.Met798Val (c.2392A>G)?

AlphaMissense predicts likely benign (score 0.054) — an in-silico prediction, not a clinical call.

CPT1C p.Met798Val

c.2392A>G · rs113511313 · VCV542770

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 4 submitters

AlphaMissense

likely benign

0.054 · ACMG-weighted

gnomAD v4.1

Rare

rare (popmax 0.41%, nfe)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

hereditary spastic paraplegia 73

Computational evidence

Protein change
AlphaMissense	0.054	likely benign
REVEL	0.132	moderately benign-leaning
SaProt	LLR -5.05	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 -0.15
Regional constraint	o/e 0.87	unconstrained · MANE · 4,824 bp · p 0.0093 · regional, not allelic
Overall
CADD	0.332	PHRED · no single calibrated threshold — expert panels disagree

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

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.41% European (non-Finnish) · 4,836/1,179,104 alleles

Filtering AF 0.4% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.396%

Overall 0.346% 5,581/1,612,116 alleles · rare

Ancestry group	Frequency	1 in
Finnishnot grpmax-eligible	0.414%	241
European (non-Finnish)grpmax	0.41%	244
Remaining individualsnot grpmax-eligible	0.348%	288
South Asian	0.168%	594
African / African-American	0.0867%	1,154
Admixed American	0.0723%	1,384
Middle Eastern	0.0166%	6,040
Ashkenazi Jewishnot grpmax-eligible	0.0034%	29,422

Finnish shows a higher raw frequency than the grpmax group above it. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and “Remaining individuals” — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.

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: CPT1C
Protein: p.Met798Val
Coding: c.2392A>G
MANE Select: NM_001199753
dbSNP: rs113511313
Type: single nucleotide variant
Location: chr19:49713585 (GRCh38)
Gene constraint: LOEUF 0.778 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 88.81 · 1 PDB
Residue 798: the 'required for interaction with gria1' region; the 'disordered' region

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

Disease context

hereditary spastic paraplegia 73 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Autosomal dominant spastic paraplegia type 73 (Orphanet):

Inheritance: Autosomal dominant
Onset: Adult

Similar variants

CPT1C c.1160+3A>G Uncertain significance ★★ same condition
CPT1C p.Ala117Val Uncertain significance ★★ ⚠ same condition
CPT1C p.Ala19Thr Uncertain significance ★★ ⚠ same condition
CPT1C p.Ala203Thr Uncertain significance ★★ ⚠ same condition
CPT1C p.Ala401Val Uncertain significance ★★ ⚠ same condition
CPT1C p.Ala422Thr Uncertain significance ★★ ⚠ same condition
CPT1C p.Ala431Val Uncertain significance ★★ ⚠ same condition
CPT1C p.Ala4Glu Uncertain significance ★★ ⚠ 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/cpt1c-p-met798val (accessed [today's date]).

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