# NM_000320.3(QDPR):c.546G>A (p.Pro182=)

https://sugi.bio/variant/qdpr-p-pro182

## Summary

**QDPR p.Pro182= (c.546G>A)** is classified **Uncertain significance** in QDPR (ClinVar, Single submitter, 1 submitter; last evaluated 2021-09-30). No allele count reported in gnomAD v4.1 (AN 1,612,830); Associated with dihydropteridine reductase deficiency.

**At a glance:** Uncertain significance · review: Single submitter · rsID rs1176312266 · 1 submitter · 1 linked condition · no allele count reported in gnomAD v4.1 (AN 1,612,830)

## For patients & families {#patients}

This is a change in the QDPR gene that is currently of uncertain significance — a definitive interpretation has not yet been established, submitted by 1 submitter, and is linked to dihydropteridine reductase 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) | Infancy, Neonatal |
| Prevalence | 1-9 / 1 000 000 (Japan) |
| Clinical trials | 1 registered for this condition — see ClinicalTrials.gov |
| Diagnostic panels | QDPR is a diagnostic-grade gene on 8 Genomics England panels |

**Commonly reported features of Hyperphenylalaninemia due to tetrahydrobiopterin deficiency** (across patients with this condition; presentation varies — frequencies from Orphanet):

- Hyperphenylalaninemia — Very frequent (99-80%)
- Atypical behavior — Frequent (79-30%)
- Hypotonia — Frequent (79-30%)
- Excessive salivation — Frequent (79-30%)
- Decreased CSF homovanillic acid concentration — Frequent (79-30%)
- Neurodevelopmental delay — Frequent (79-30%)
- Abnormal circulating neopterin concentration — Frequent (79-30%)
- Abnormal circulating biopterin concentration — Frequent (79-30%)

**Support & next steps:** [Condition overview & support (NIH GARD)](https://rarediseases.info.nih.gov/diseases/0004319/index) · [Find a genetic counselor (NSGC)](https://findageneticcounselor.nsgc.org/).

## Identity {#identity}

| Field | Value |
| --- | --- |
| Gene | [QDPR](https://sugi.bio/atlas/gene/QDPR/) |
| Protein change (HGVS p.) | p.Pro182= |
| Coding change (HGVS c.) | c.546G>A |
| MANE Select transcript | [NM_000320](https://www.ncbi.nlm.nih.gov/nuccore/NM_000320) |
| dbSNP | [rs1176312266](https://www.ncbi.nlm.nih.gov/snp/rs1176312266/) |
| Variant type | single nucleotide variant |
| Location | chr4:17490745-17490745 (GRCh38) |
| ClinVar | [VCV1036861](https://www.ncbi.nlm.nih.gov/clinvar/variation/1036861/) |

**All HGVS expressions:** `NC_000004.11:g.17492368C>T`, `NC_000004.12:g.17490745C>T`, `NG_008763.1:g.26490G>A`, `NM_000320.3:c.546G>A`, `NM_001306140.2:c.453G>A`, `NR_156494.2:n.473G>A`

## Computational & population evidence {#evidence}

**Concordance:** Mixed / partial computational evidence (see below).

- **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 0.558, GERP 0.125, phastCons 0.997 — weakly conserved position
- CADD: **PHRED 15.4**. 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.*
- 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: **no allele count reported in gnomAD v4.1 (AN 1,612,830)** — 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}

**QDPR** population constraint: LOEUF 0.984, pLI 4.011e-06, missense-Z 0.32789. *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):

- **dihydropteridine reductase deficiency** — Definitive (AR)

## Protein context {#protein}


AlphaFold model confidence (whole protein): pLDDT 96.43, 96% of residues very-high.

**2 experimental structure(s)** (PDB): [1HDR](https://www.rcsb.org/structure/1HDR), [9DTW](https://www.rcsb.org/structure/9DTW).

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

*Describes the biological roles of QDPR (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:** QDPR's established molecular role includes 6,7-dihydropteridine reductase activity.


### Pathways affected {#pathways}

QDPR participates in **1 Reactome pathway** (⚕ = disease pathway):

| Pathway (Reactome) | Evidence |
| --- | --- |
| [Phenylalanine metabolism](https://reactome.org/content/detail/R-HSA-8964208) | curated |

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

**Molecular function:** 6,7-dihydropteridine reductase activity.

## Clinical significance {#significance}

**Uncertain significance** — review status Single submitter *(criteria provided, single submitter)*, last evaluated 2021-09-30.

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

### Submitter classifications {#submitters}

| Submitter | Classification | Review | Method | Date |
| --- | --- | --- | --- | --- |
| Labcorp Genetics (formerly Invitae), Labcorp | Uncertain significance | criteria provided, single submitter | clinical testing | 2021-09-30 |

## Associated conditions {#conditions}

[dihydropteridine reductase deficiency](https://sugi.bio/atlas/disease/dihydropteridine-reductase-deficiency/).

**Reported phenotype names (ClinVar):** Dihydropteridine reductase deficiency, DHPR DEFICIENCY, BH4-Deficient Hyperphenylalaninemia C, HYPERPHENYLALANINEMIA, TETRAHYDROBIOPTERIN-DEFICIENT, DUE TO DHPR DEFICIENCY, QDPR DEFICIENCY, QUINOID DIHYDROPTERIDINE REDUCTASE DEFICIENCY, Phenylketonuria II, Hyperphenylalaninemia due to dihydropteridine reductase deficiency, Hyperphenylalaninemia, BH-4-deficient, C, Phenylketonuria type 2.

## Same-residue context {#hotspot}

Residue **182** carries **1 other pathogenic ClinVar variant** — a recurrently-mutated position: [QDPR p.Pro182Arg](/variant/qdpr-p-pro182arg). *Positional co-occurrence of independent ClinVar records, not functional proof.*

## Similar variants {#similar}

Related QDPR variant pages (same residue, condition, or type): [QDPR p.Pro182Arg](/variant/qdpr-p-pro182arg), [QDPR p.Pro182Leu](/variant/qdpr-p-pro182leu), [QDPR c.436+2552A>G](/variant/qdpr-c-436-plus-2552a-g), [QDPR c.545+1G>A](/variant/qdpr-c-545-plus-1g-a), [QDPR c.546-1G>A](/variant/qdpr-c-546-minus-1g-a), [QDPR p.Arg221Ter](/variant/qdpr-p-arg221ter), [QDPR p.His158Tyr](/variant/qdpr-p-his158tyr), [QDPR p.Phe212Ser](/variant/qdpr-p-phe212ser).

### 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 1036861). 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.*