Is CPT1A p.Met643Val (c.1927A>G) pathogenic?

CPT1A p.Met643Val (c.1927A>G) is classified Uncertain significance in CPT1A (ClinVar, Single submitter, 1 submitter; last evaluated 2023-12-15). AlphaMissense: likely benign (0.1689); Very rare (popmax 0.00267%, afr); Associated with Inborn genetic diseases.

What condition is associated with CPT1A p.Met643Val (c.1927A>G)?

CPT1A p.Met643Val (c.1927A>G) is associated with Inborn genetic diseases (ClinVar).

How common is CPT1A p.Met643Val (c.1927A>G) in the general population?

CPT1A p.Met643Val (c.1927A>G) is very rare (popmax 0.00267%, afr) (gnomAD).

What do computational predictors say about CPT1A p.Met643Val (c.1927A>G)?

AlphaMissense predicts likely benign (score 0.1689) — an in-silico prediction, not a clinical call.

CPT1A p.Met643Val

c.1927A>G · rs375814998 · VCV3076913

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1689 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00267%, afr)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.1689	likely benign
REVEL	0.247	benign-leaning
SaProt	LLR -8.74	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 -0.4	GERP -4.1
Regional constraint	o/e 0.78	unconstrained · MANE · 46 kb · p 1.1e-09 · regional, not allelic
Overall
CADD	9.466	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

Grpmax group 0.00267% African / African-American · 2/74,908 alleles

Filtering AF 0.0013% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00108%

Overall 0.00155% 25/1,614,020 alleles · very rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.00267%	37,454
European (non-Finnish)	0.00195%	51,306

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: CPT1A
Protein: p.Met643Val
Coding: c.1927A>G
MANE Select: NM_001876
dbSNP: rs375814998
Type: single nucleotide variant
Location: chr11:68761636 (GRCh38)
Gene constraint: LOEUF 0.709 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 92.55 · 1 PDB

Full CPT1A gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

CPT1A p.Arg395Pro Likely pathogenic ★★ same condition
CPT1A c.2029-3T>C Uncertain significance ★★ same condition
CPT1A p.Ala499Val Uncertain significance ★★ ⚠ same condition
CPT1A p.Ala568Ser Uncertain significance ★★ ⚠ same condition
CPT1A p.Arg173Cys Uncertain significance ★★ ⚠ same condition
CPT1A p.Arg201Gln Uncertain significance ★★ ⚠ same condition
CPT1A p.Arg401Cys Uncertain significance ★★ ⚠ same condition
CPT1A p.Arg595Gln 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/cpt1a-p-met643val (accessed [today's date]).

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