# NM_000277.3(PAH):c.993T>C (p.Phe331=)

https://sugi.bio/variant/pah-p-phe331

## Summary

**PAH p.Phe331= (c.993T>C)** is classified **Likely benign** in PAH (ClinVar, Single submitter, 1 submitter; last evaluated 2022-05-28). Very rare (popmax 8.48e-05%, nfe); Associated with phenylketonuria.

**At a glance:** Likely benign · review: Single submitter · rsID rs2499615169 · 1 submitter · 1 linked condition · very rare (popmax 8.48e-05%, nfe)

## For patients & families {#patients}

This is a change in the PAH gene that is classified as likely benign — not considered disease-causing, submitted by 1 submitter, and is linked to phenylketonuria.

*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 |
| Prevalence | 1-9 / 100 000 (France) |
| Clinical trials | 176 registered for this condition — see ClinicalTrials.gov |
| Diagnostic panels | PAH is a diagnostic-grade gene on 11 Genomics England panels |

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

- Phenylalaninuria — Very frequent (99-80%)
- Microcephaly — Frequent (79-30%)
- Atypical behavior — Frequent (79-30%)
- Osteopenia — Frequent (79-30%)
- Eczematoid dermatitis — Frequent (79-30%)
- Hypopigmentation of the skin — Frequent (79-30%)
- Seizure — Frequent (79-30%)
- Global developmental delay — Frequent (79-30%)

**Support & next steps:** [Condition overview & support (NIH GARD)](https://rarediseases.info.nih.gov/diseases/0007383/index) · [Find a genetic counselor (NSGC)](https://findageneticcounselor.nsgc.org/).

## Identity {#identity}

| Field | Value |
| --- | --- |
| Gene | [PAH](https://sugi.bio/atlas/gene/PAH/) |
| Protein change (HGVS p.) | p.Phe331= |
| Coding change (HGVS c.) | c.993T>C |
| MANE Select transcript | [NM_000277](https://www.ncbi.nlm.nih.gov/nuccore/NM_000277) |
| dbSNP | [rs2499615169](https://www.ncbi.nlm.nih.gov/snp/rs2499615169/) |
| Variant type | single nucleotide variant |
| Location | chr12:102844408-102844408 (GRCh38) |
| ClinVar | [VCV2153068](https://www.ncbi.nlm.nih.gov/clinvar/variation/2153068/) |

**All HGVS expressions:** `NC_000012.11:g.103238186A>G`, `NC_000012.12:g.102844408A>G`, `NG_008690.2:g.119003T>C`, `NM_000277.3:c.993T>C`, `NM_001354304.2:c.993T>C`

## 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 1.917, GERP -0.199, phastCons 1 — weakly conserved position
- CADD: **PHRED 8.965**. 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: **below the reporting threshold**. This position is scored for a different substitution (A>T, Δ0.36 acceptor loss), so this allele was evaluated and its deltas all fell under Δ0.2 — a prediction of no splicing effect for this allele, not a gap in our data. *No ACMG code assigned.*
- Population frequency (gnomAD v4.1): grpmax **8.48e-05%** (nfe) · 1/1,179,514 in the highest group · 1/1,461,188 alleles overall — very rare (popmax 8.48e-05%, nfe).

*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}

**PAH** population constraint: LOEUF 1.265, pLI 9.0947e-20, missense-Z -0.00030735; ClinGen dosage — haploinsufficiency 30, triplosensitivity 0 (0–3 scale). *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):

- **phenylketonuria** — Definitive (AR)

## Protein context {#protein}

Residue **331** lies in a UniProt-annotated variant site (in pah deficiency; severe).

AlphaFold model confidence (whole protein): pLDDT 89.04, 63% of residues very-high.

**21 experimental structure(s)** (PDB): [1DMW](https://www.rcsb.org/structure/1DMW), [1J8T](https://www.rcsb.org/structure/1J8T), [1J8U](https://www.rcsb.org/structure/1J8U), [1KW0](https://www.rcsb.org/structure/1KW0), [1LRM](https://www.rcsb.org/structure/1LRM), [1MMK](https://www.rcsb.org/structure/1MMK) — incl. mutant structure 1TDW.

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

*Describes the biological roles of PAH (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:** PAH's established molecular role includes phenylalanine 4-monooxygenase activity. In Reactome, PAH is annotated in disease pathway(s) including **Phenylketonuria**.

**Disease mechanism (Reactome):** PAH loss or alteration is curated in [Phenylketonuria](https://reactome.org/content/detail/R-HSA-2160456).

### Pathways affected {#pathways}

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

| Pathway (Reactome) | Evidence |
| --- | --- |
| ⚕ [Phenylketonuria](https://reactome.org/content/detail/R-HSA-2160456) | curated |
| [Phenylalanine metabolism](https://reactome.org/content/detail/R-HSA-8964208) | curated |

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

**Molecular function:** phenylalanine 4-monooxygenase activity.

## Clinical significance {#significance}

**Likely benign** — review status Single submitter *(criteria provided, single submitter)*, last evaluated 2022-05-28.

**Submitter consensus:** unanimous (1/1 Likely benign).

### Submitter classifications {#submitters}

| Submitter | Classification | Review | Method | Date |
| --- | --- | --- | --- | --- |
| Labcorp Genetics (formerly Invitae), Labcorp | Likely benign | criteria provided, single submitter | clinical testing | 2022-05-28 |

## Associated conditions {#conditions}

[phenylketonuria](https://sugi.bio/atlas/disease/phenylketonuria/).

**Reported phenotype names (ClinVar):** Phenylketonuria, FOLLING DISEASE, OLIGOPHRENIA PHENYLPYRUVICA, Phenylketonurias, Phenylalanine Hydroxylase Deficiency.

## Same-residue context {#hotspot}

Residue **331** carries **2 other pathogenic ClinVar variants** — a recurrently-mutated position: [PAH p.Phe331Cys](/variant/pah-p-phe331cys), [PAH p.Phe331Ser](/variant/pah-p-phe331ser). *Positional co-occurrence of independent ClinVar records, not functional proof.*

## Similar variants {#similar}

Related PAH variant pages (same residue, condition, or type): [PAH p.Phe331Cys](/variant/pah-p-phe331cys), [PAH p.Phe331Ser](/variant/pah-p-phe331ser), [PAH c.1065+1G>A](/variant/pah-c-1065-plus-1g-a), [PAH c.1065+1G>T](/variant/pah-c-1065-plus-1g-t), [PAH c.1065+3A>G](/variant/pah-c-1065-plus-3a-g), [PAH c.1066-11G>A](/variant/pah-c-1066-minus-11g-a), [PAH c.1066-14C>G](/variant/pah-c-1066-minus-14c-g), [PAH c.1066-1G>A](/variant/pah-c-1066-minus-1g-a).

### Data sources & attribution {#sources}

ClinVar (NCBI — public domain, built 2026-10-11); 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 2153068). 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.*