Is CPT1A p.Pro510= (c.1530G>A) pathogenic?

CPT1A p.Pro510= (c.1530G>A) is classified Likely benign in CPT1A (ClinVar, Single submitter, 1 submitter; last evaluated 2024-04-08). Ultra-rare (popmax 0.033%, mid); Associated with carnitine palmitoyl transferase 1A deficiency.

What condition is associated with CPT1A p.Pro510= (c.1530G>A)?

CPT1A p.Pro510= (c.1530G>A) is associated with carnitine palmitoyl transferase 1A deficiency (ClinVar).

How common is CPT1A p.Pro510= (c.1530G>A) in the general population?

CPT1A p.Pro510= (c.1530G>A) is ultra-rare (popmax 0.033%, mid) (gnomAD).

How is Carnitine palmitoyl transferase 1A deficiency inherited?

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

CPT1A p.Pro510=

c.1530G>A · rs141303589 · VCV1139996

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.033%, mid)

Conditions

carnitine palmitoyl transferase 1A deficiency

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 -6.5	GERP -4.1
Overall
CADD	1.467	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.033% Middle Eastern · 2/6,062 alleles

Filtering AF 0.00582% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00242%

Overall 0.00173% 28/1,614,206 alleles · ultra-rare

Ancestry group	Frequency	1 in
Middle Easterngrpmax	0.033%	3,031
East Asian	0.00668%	14,963
South Asian	0.00549%	18,216
Remaining individualsnot grpmax-eligible	0.0032%	31,256
African / African-American	0.00266%	37,527
Admixed American	0.00167%	60,022
Finnishnot grpmax-eligible	0.00156%	64,040
European (non-Finnish)	0.00102%	98,335

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.Pro510=
Coding: c.1530G>A
MANE Select: NM_001876
dbSNP: rs141303589
Type: single nucleotide variant
Location: chr11:68775361 (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

carnitine palmitoyl transferase 1A deficiency — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Carnitine palmitoyl transferase 1A deficiency (Orphanet):

Inheritance: Autosomal recessive
Onset: Infancy, Neonatal

Similar variants

CPT1A p.Pro510Leu Benign ★★ same residue
CPT1A p.Pro510Ala Uncertain significance ★ ⚠ same residue
CPT1A p.Pro510Ser Uncertain significance ★ ⚠ same residue
CPT1A p.Pro510Thr Uncertain significance ★ ⚠ same residue
CPT1A c.1163+1G>A Pathogenic/Likely pathogenic ★★ same condition
CPT1A c.1163+2T>C Pathogenic/Likely pathogenic ★★ same condition
CPT1A c.1352+1G>C Likely pathogenic ★★ same condition
CPT1A c.1459-1G>A Likely pathogenic ★★ 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-pro510 (accessed [today's date]).

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