# NM_001040716.2(PC):c.1997C>T (p.Ala666Val)

https://sugi.bio/variant/pc-p-ala666val

## Summary

**PC p.Ala666Val (c.1997C>T)** is classified **Uncertain significance** in PC (ClinVar, Single submitter, 1 submitter; last evaluated 2023-06-30). AlphaMissense: likely pathogenic (0.8829); Very rare (popmax 0.00667%, afr).

**At a glance:** Uncertain significance · review: Single submitter · 1 submitter · AlphaMissense likely pathogenic · very rare (popmax 0.00667%, afr)

## For patients & families {#patients}

This is a change in the PC gene that is currently of uncertain significance — a definitive interpretation has not yet been established, submitted by 1 submitter.

*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.*

**Support & next steps:** [Find a genetic counselor (NSGC)](https://findageneticcounselor.nsgc.org/).

## Identity {#identity}

| Field | Value |
| --- | --- |
| Gene | [PC](https://sugi.bio/atlas/gene/PC/) |
| Protein change (HGVS p.) | p.Ala666Val |
| Coding change (HGVS c.) | c.1997C>T |
| MANE Select transcript | [NM_001040716](https://www.ncbi.nlm.nih.gov/nuccore/NM_001040716) |
| Variant type | single nucleotide variant |
| Location | chr11:66851266-66851266 (GRCh38) |
| ClinVar | [VCV3380032](https://www.ncbi.nlm.nih.gov/clinvar/variation/3380032/) |

**All HGVS expressions:** `NC_000011.10:g.66851266G>A`, `NC_000011.9:g.66618737G>A`, `NG_008319.1:g.112111C>T`, `NG_123025.1:g.543G>A`, `NM_000920.4:c.1997C>T`, `NM_001040716.2:c.1997C>T`, `NM_022172.3:c.1997C>T`

## Computational & population evidence {#evidence}

**Concordance:** ClinVar classifies this **uncertain**; the computational predictors unanimously lean **damaging** — a triage signal, not a reclassification.

- AlphaMissense **likely pathogenic** (0.8829)
- REVEL 0.907 (moderately pathogenic-leaning) — agrees with AlphaMissense
- SaProt LLR -10.852 (damaging) — agrees with AlphaMissense
- → **In-silico consensus:** AlphaMissense, REVEL and SaProt all call this damaging
- Conservation: phyloP 11.681, GERP 1.38, phastCons 1 — highly conserved (agrees)
- CADD: **PHRED 25.5**. No single ClinGen-calibrated threshold exists and the expert panels that use CADD disagree — GUCY2D/AIPL1 require ≥ 20.0 for an untranslated-region variant, ABCA4 ≥ 28.1 for a synonymous or indel variant, the Pulmonary Hypertension panel imports Pejaver 2022's missense-calibrated numbers, and the Antibody Deficiencies panel declines CADD entirely for PIK3CD. CADD v1.7 also incorporates Zoonomia phyloP, so it partly re-expresses the conservation above. *Descriptive; no threshold applied.*
- Regional missense constraint: **o/e 0.74** across the covering region of the MANE Select transcript (66,849,101–66,872,159), spanning 23,058 bp. Chi-square p 3.1e-25. Describes the region, not this allele; gnomAD v4.1.1's own constrained determination. *Descriptive; no ACMG code applied.*
- SpliceAI: **not assessed** — no allele at this position is in our SpliceAI release, either because it lies outside the scored MANE transcript scope or because every allele is below Δ0.2. We cannot tell which, so this claims neither; absence is not evidence against a splicing effect.
- Population frequency (gnomAD v4.1): grpmax **0.00667%** (afr) · FAF95 0.00255% · FAF99 0.00161% · 5/74,920 in the highest group · 5/1,600,986 alleles overall — very rare (popmax 0.00667%, afr).

*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}

**PC** population constraint: LOEUF 0.539, pLI 0.065118, missense-Z 3.7757; ClinGen dosage — haploinsufficiency gene assoc. with recessive phenotype, triplosensitivity Not yet evaluated/3. *Lower LOEUF and higher pLI indicate a gene that tolerates loss-of-function poorly; ClinGen dosage is the curated haploinsufficiency call.*

## Protein context {#protein}

Residue **666** lies in an α-helix; the pyruvate carboxyltransferase domain.

AlphaFold model confidence (whole protein): pLDDT 90.53, 71% of residues very-high.

**10 experimental structure(s)** (PDB): [3BG3](https://www.rcsb.org/structure/3BG3), [3BG9](https://www.rcsb.org/structure/3BG9), [7WTA](https://www.rcsb.org/structure/7WTA), [7WTB](https://www.rcsb.org/structure/7WTB), [7WTC](https://www.rcsb.org/structure/7WTC), [7WTD](https://www.rcsb.org/structure/7WTD) — incl. mutant structure 3BG9.

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

*Describes the biological roles of PC (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:** PC's established molecular role includes pyruvate carboxylase activity. p.Ala666Val falls in the pyruvate carboxyltransferase domain. In Reactome, PC is annotated in disease pathway(s) including **Defective HLCS causes multiple carboxylase deficiency**.

**Disease mechanism (Reactome):** PC loss or alteration is curated in [Defective HLCS causes multiple carboxylase deficiency](https://reactome.org/content/detail/R-HSA-3371599).

### Pathways affected {#pathways}

PC participates in **4 Reactome pathways** (⚕ = disease pathway):

| Pathway (Reactome) | Evidence |
| --- | --- |
| ⚕ [Defective HLCS causes multiple carboxylase deficiency](https://reactome.org/content/detail/R-HSA-3371599) | curated |
| [Biotin transport and metabolism](https://reactome.org/content/detail/R-HSA-196780) | curated |
| [Gluconeogenesis](https://reactome.org/content/detail/R-HSA-70263) | curated |
| [Pyruvate metabolism](https://reactome.org/content/detail/R-HSA-70268) | curated |

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

**Molecular function:** pyruvate carboxylase activity, identical protein binding.

**Biological process:** NADP+ metabolic process, negative regulation of gene expression, viral RNA genome packaging, viral release from host cell, NAD+ metabolic process, host-mediated activation of viral process.

## Clinical significance {#significance}

**Uncertain significance** — review status Single submitter *(criteria provided, single submitter)*, last evaluated 2023-06-30.

**Submitter consensus:** unanimous (1/1 Uncertain significance).

### Submitter classifications {#submitters}

| Submitter | Classification | Review | Method | Date |
| --- | --- | --- | --- | --- |
| Mayo Clinic Laboratories, Mayo Clinic | Uncertain significance | criteria provided, single submitter | clinical testing | 2023-06-30 |

**Reported phenotype names (ClinVar):** not provided, none provided, RECLASSIFIED - ADRA2C POLYMORPHISM, RECLASSIFIED - ADRB1 POLYMORPHISM.

## Similar variants {#similar}

Related PC variant pages (same residue, condition, or type): [PC p.Ala666Ser](/variant/pc-p-ala666ser), [PC c.1368+1G>A](/variant/pc-c-1368-plus-1g-a), [PC c.1826-1G>C](/variant/pc-c-1826-minus-1g-c), [PC c.1983-116C>T](/variant/pc-c-1983-minus-116c-t), [PC c.633+2T>C](/variant/pc-c-633-plus-2t-c), [PC p.Ala610Thr](/variant/pc-p-ala610thr), [PC p.Ala812Asp](/variant/pc-p-ala812asp), [PC p.Arg18Ter](/variant/pc-p-arg18ter).

### 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 2026-10-14); 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 3380032). 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.*