# NM_000098.3(CPT2):c.627_630dup (p.Pro211fs)

https://sugi.bio/variant/cpt2-p-pro211fs

## Summary

**CPT2 p.Pro211fs (c.627_630dup)** is classified **Pathogenic/Likely pathogenic** in CPT2 (ClinVar, Multiple submitters, 4 submitters; last evaluated 2024-02-27). No gnomAD frequency available for this variant; Associated with carnitine palmitoyltransferase II deficiency.

**At a glance:** Pathogenic/Likely pathogenic · review: Multiple submitters · rsID rs1553169629 · 4 submitters · 3 linked conditions · no gnomAD frequency available for this variant

## For patients & families {#patients}

This is a change in the CPT2 gene that is considered likely disease-causing, submitted by 4 submitters, and is linked to carnitine palmitoyltransferase II deficiency.

*Reference information, not medical advice, and not a prediction for any individual. A genetic counselor or clinician can interpret what it means for you and your family.*

|  |  |
| --- | --- |
| Typical inheritance (of this condition) | Autosomal recessive |
| Age of onset (of this condition) | All ages |
| Clinical trials | 5 registered for this condition — see ClinicalTrials.gov |
| Diagnostic panels | CPT2 is a diagnostic-grade gene on 13 Genomics England panels |

**Commonly reported features of Carnitine palmitoyltransferase II deficiency** (across patients with this condition; presentation varies — frequencies from Orphanet):

- Muscle weakness — Very frequent (99-80%)
- Myalgia — Very frequent (99-80%)
- Reduced carnitine O-palmitoyltransferase activity — Very frequent (99-80%)
- Myoglobinuria — Frequent (79-30%)
- Hyperlipidemia — Frequent (79-30%)
- Myopathy — Frequent (79-30%)
- Elevated circulating creatine kinase concentration — Frequent (79-30%)
- Exercise intolerance — Frequent (79-30%)

**Support & next steps:** [Condition overview & support (NIH GARD)](https://rarediseases.info.nih.gov/diseases/0001121/index) · [Find a genetic counselor (NSGC)](https://findageneticcounselor.nsgc.org/).

## Identity {#identity}

| Field | Value |
| --- | --- |
| Gene | [CPT2](https://sugi.bio/atlas/gene/CPT2/) |
| Protein change (HGVS p.) | p.Pro211fs |
| Coding change (HGVS c.) | c.627_630dup |
| MANE Select transcript | [NM_000098](https://www.ncbi.nlm.nih.gov/nuccore/NM_000098) |
| dbSNP | [rs1553169629](https://www.ncbi.nlm.nih.gov/snp/rs1553169629/) |
| Variant type | Duplication |
| Location | chr1:53210300-53210301 (GRCh38) |
| ClinVar | [VCV554042](https://www.ncbi.nlm.nih.gov/clinvar/variation/554042/) |

**All HGVS expressions:** `NC_000001.10:g.53675973_53675976dup`, `NC_000001.11:g.53210301_53210304dup`, `NG_008035.1:g.18873_18876dup`, `NM_000098.2:c.627_630dupGTAT`, `NM_000098.3:c.627_630dup`, `NM_001330589.2:c.627_630dup`

## Computational & population evidence {#evidence}

**Concordance:** 1 independent predictor **concordant** with the ClinVar classification.

- **Missense predictors (AlphaMissense/REVEL/SaProt) do not apply** to this variant type — they score amino-acid substitutions only. For non-missense variants the computational signal comes from conservation (below), not from a missing predictor score.
- Conservation: phyloP 5.971, GERP 2.23, phastCons 1 — highly conserved position (PP3-type support)
- Molecular consequence: **frameshift** — a predicted loss-of-function variant. Gene population constraint: LOEUF 1.038, pLI 1.9677e-09. *Descriptive; not an applied PVS1 code.*
- Nonsense-mediated decay: the premature termination codon is **in exon 4 of 5**, so the transcript is predicted to undergo NMD.
- SpliceAI: **not assessed** — the release is built from a substitutions-only source, so it holds no duplication variants. That is a property of the dataset, not of the variant, and is not evidence against a splicing effect.
- Population frequency: **no gnomAD frequency available for this variant** — rarity (ACMG PM2) and BA1/BS1 cannot be assessed for this variant.

*Computational predictors are not independent (ClinGen Variant Classification guidance): AlphaMissense (Cheng et al. 2023) carries the ACMG weight for missense and conservation (phyloP/GERP/phastCons) for non-missense; REVEL (Pejaver-2022 calibrated strength bands) and SaProt (Su et al. 2023, structure-aware, ClinVar-independent protein language model, raw LLR) are shown as orthogonal agreement signals, not additive. For frequency, the gnomAD v4.1 grpmax filtering allele frequency (FAF95) is ClinGen's designated BA1/BS1 input (gnomAD v4 guidance v3.0, June 2025); BA1/BS1 thresholds are disease-specific, not a blanket 5%. Predictions, not a clinical determination.*

## Gene constraint & dosage {#gene-context}

**CPT2** population constraint: LOEUF 1.038, pLI 1.9677e-09, missense-Z 0.75528. *Lower LOEUF and higher pLI indicate a gene that tolerates loss-of-function poorly; ClinGen dosage is the curated haploinsufficiency call.*

Curated gene–disease validity (ClinGen):

- **carnitine palmitoyltransferase II deficiency** — Definitive (AR)

## Protein context {#protein}


AlphaFold model confidence (whole protein): pLDDT 94.52, 93% of residues very-high.

## What this gene does {#gene-function}

*Describes the biological roles of CPT2 (the gene this variant disrupts) — not effects measured for this specific variant. A damaging variant is expected to affect these functions and pathways; the degree depends on the variant.*

**How this variant is thought to act:** CPT2's established molecular role includes carnitine O-palmitoyltransferase activity.


### Pathways affected {#pathways}

CPT2 participates in **2 Reactome pathways** (⚕ = disease pathway):

| Pathway (Reactome) | Evidence |
| --- | --- |
| [Carnitine shuttle](https://reactome.org/content/detail/R-HSA-200425) | curated |
| [PPARA activates gene expression](https://reactome.org/content/detail/R-HSA-1989781) | curated |

### Molecular function & processes (GO — experimentally supported) {#go}

**Molecular function:** carnitine O-palmitoyltransferase activity, acyltransferase activity.

**Biological process:** long-chain fatty acid metabolic process, fatty acid beta-oxidation, carnitine metabolic process.

## Clinical significance {#significance}

**Pathogenic/Likely pathogenic** — review status Multiple submitters *(criteria provided, multiple submitters, no conflicts)*, last evaluated 2024-02-27.

**Submitter consensus:** conflicting (3 Likely pathogenic, 1 Pathogenic).

**Submission history:** 4 submissions (2017–2024); classifications have differed over time.

### Submitter classifications {#submitters}

| Submitter | Classification | Review | Method | Date |
| --- | --- | --- | --- | --- |
| Counsyl | Likely pathogenic | no assertion criteria provided | clinical testing | 2017-10-06 |
| Baylor Genetics | Likely pathogenic | criteria provided, single submitter | clinical testing | 2024-02-27 |
| Genome-Nilou Lab | Likely pathogenic | criteria provided, single submitter | clinical testing | 2023-04-11 |
| Labcorp Genetics (formerly Invitae), Labcorp | Pathogenic | criteria provided, single submitter | clinical testing | 2022-03-12 |

## Associated conditions {#conditions}

[carnitine palmitoyltransferase II deficiency](https://sugi.bio/atlas/disease/carnitine-palmitoyltransferase-ii-deficiency/), [carnitine palmitoyl transferase II deficiency, severe infantile form](https://sugi.bio/atlas/disease/carnitine-palmitoyl-transferase-ii-deficiency-severe-infantile-form/), [encephalopathy, acute, infection-induced, susceptibility to, 4](https://sugi.bio/atlas/disease/encephalopathy-acute-infection-induced-susceptibility-to-4/).

**Reported phenotype names (ClinVar):** Carnitine palmitoyltransferase II deficiency, Carnitine palmitoyl transferase II deficiency, severe infantile form, Encephalopathy, acute, infection-induced, susceptibility to, 4, Carnitine Palmitoyltransferase 2 Deficiency, CARNITINE PALMITOYLTRANSFERASE II DEFICIENCY WITH HYPOKETOTIC HYPOGLYCEMIA, CARNITINE PALMITOYLTRANSFERASE II DEFICIENCY, HEPATOCARDIOMUSCULAR, CPT II DEFICIENCY, HEPATIC, CPT2 DEFICIENCY, INFANTILE, CPT II deficiency, infantile.

## Similar variants {#similar}

Related CPT2 variant pages (same residue, condition, or type): [CPT2 p.Pro211Ser](/variant/cpt2-p-pro211ser), [CPT2 p.Pro211=](/variant/cpt2-p-pro211), [CPT2 p.Arg303fs](/variant/cpt2-p-arg303fs), [CPT2 p.Asn349fs](/variant/cpt2-p-asn349fs), [CPT2 p.Asp279fs](/variant/cpt2-p-asp279fs), [CPT2 p.His242fs](/variant/cpt2-p-his242fs), [CPT2 p.Lys537fs](/variant/cpt2-p-lys537fs), [CPT2 p.Thr442fs](/variant/cpt2-p-thr442fs).

### Data sources & attribution {#sources}

ClinVar (NCBI — public domain, built 2026-10-14); gnomAD v4.1 (Broad Institute, built 2026-10-06); AlphaMissense (Cheng et al. 2023, © Google DeepMind — CC BY 4.0, built 2026-01-27); REVEL (Ioannidis et al. 2016 — ODbL, built 2026-07-13); SaProt (Su et al. 2023 — MIT, built 2026-07-14); SpliceAI (Illumina — free for non-commercial use, built 2026-10-13); CADD (Rentzsch et al. 2019, University of Washington — free for non-commercial use, built 2026-10-10); Conservation (phyloP/phastCons/GERP) (UCSC hg38 470-way mammal (Hiller Lab) + Ensembl Compara, built 2026-07-12); gnomAD Non-coding Constraint (Gnocchi) (Chen et al. 2024, Broad Institute — CC0, built 2026-10-11); gnomAD Regional Missense Constraint (Broad Institute — CC0, built 2026-10-13); Pangolin (Zeng & Li 2022 — CC BY 4.0, built 2026-10-11); Repeat regions (UCSC — RepeatMasker, TRF, segmental duplications, built 2026-10-11); ClinGen (ClinGen, built 2026-09-22); UniProt (CC BY 4.0); Reactome / GO (CC BY 4.0, built 2026-09-23); MaveDB (per-record license, built 2026-10-11); CIViC (CC0, built 2026-09-22); Orphanet (Orphanet, built 2026-06-12)

*Primary record: NCBI ClinVar (variation 554042). Classifications reflect these databases as of the page's build date and may change. Free reference use — not medical advice; consult the primary submitters and a clinician.*