# NM_000311.5(PRNP):c.180T>C (p.Pro60=)

https://sugi.bio/variant/prnp-p-pro60

## Summary

**PRNP p.Pro60= (c.180T>C)** is classified **Uncertain significance** in PRNP (ClinVar, Single submitter, 1 submitter; last evaluated 2016-06-26). Very rare (popmax 0.00017%, nfe); Associated with spongiform encephalopathy with neuropsychiatric features.

**At a glance:** Uncertain significance · review: Single submitter · rsID rs1386720703 · 1 submitter · 1 linked condition · very rare (popmax 0.00017%, nfe)

## For patients & families {#patients}

This is a change in the PRNP gene that is currently of uncertain significance — a definitive interpretation has not yet been established, submitted by 1 submitter, and is linked to spongiform encephalopathy with neuropsychiatric features.

*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:** [Condition overview & support (NIH GARD)](https://rarediseases.info.nih.gov/diseases/0024819/index) · [Find a genetic counselor (NSGC)](https://findageneticcounselor.nsgc.org/).

## Identity {#identity}

| Field | Value |
| --- | --- |
| Gene | [PRNP](https://sugi.bio/atlas/gene/PRNP/) |
| Protein change (HGVS p.) | p.Pro60= |
| Coding change (HGVS c.) | c.180T>C |
| MANE Select transcript | [NM_000311](https://www.ncbi.nlm.nih.gov/nuccore/NM_000311) |
| dbSNP | [rs1386720703](https://www.ncbi.nlm.nih.gov/snp/rs1386720703/) |
| Variant type | single nucleotide variant |
| Location | chr20:4699400-4699400 (GRCh38) |
| ClinVar | [VCV453305](https://www.ncbi.nlm.nih.gov/clinvar/variation/453305/) |

**All HGVS expressions:** `NC_000020.10:g.4680046T>C`, `NC_000020.11:g.4699400T>C`, `NG_009087.1:g.18250T>C`, `NM_000311.5:c.180T>C`, `NM_001080121.3:c.180T>C`, `NM_001080122.3:c.180T>C`, `NM_001080123.3:c.180T>C`, `NM_001271561.3:c.91T>C`, `NM_183079.4:c.180T>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 -0.957, GERP -2.87 — not a conserved position (phyloP < 0.1, ACGS BP7 cut)
- CADD: **PHRED 6.986**. 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: **no splice effect predicted**. SpliceAI outputs four numbers per variant, not one: acceptor loss, donor loss, acceptor gain, donor gain (DS_AL / DS_DL / DS_AG / DS_DG). A loss score is an existing splice site weakened or destroyed; a gain score is a new site created or an existing one strengthened. The release publishes its own filter rule, which we read from the dataset rather than assume: an allele is reported only if the largest of its four deltas reaches 0.2. No allele at this position is in the release, so all four are under 0.2 for every alternate allele here. No figure is shown because none was read: the bound is deduced from that absence. It is a result, not a gap in our data, because the release scores every possible substitution across the transcripts it covers (Ensembl MANE v1.4) before it filters, so what survives for a gene is one continuous stretch. What is measured is that this position sits inside the stretch covered for PRNP (128 scored positions, the nearest 185 bases away); what is taken from the release's own description, rather than measured, is that coverage inside that stretch is continuous. On that, SpliceAI did score it. *ClinGen's SVI treats the largest of the four as evidence against a splicing effect at or below 0.1, where it may support BP4, and as uninformative between 0.1 and 0.2. We cannot tell which applies here, so these SpliceAI data support neither BP4 nor PP3; that is a statement about this evidence alone, not about the variant's other evidence.*
- Population frequency (gnomAD v4.1): grpmax **0.00017%** (nfe) · FAF95 2.8e-05% · FAF99 1.1e-05% · 2/1,176,810 in the highest group · 2/1,606,144 alleles overall — very rare (popmax 0.00017%, 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}

**PRNP** population constraint: LOEUF 1.036, pLI 0.00032327, missense-Z 1.4439. *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 **60** lies in the 'disordered' region; the '5 x 8 aa tandem repeats of p-h-g-g-g-w-g-q' region; a UniProt-annotated variant site (sequence variant); the 'interaction with grb2, eri3 and syn1' region.

AlphaFold model confidence (whole protein): pLDDT 68.18, 0% of residues very-high.

**70 experimental structure(s)** (PDB): [1E1G](https://www.rcsb.org/structure/1E1G), [1E1J](https://www.rcsb.org/structure/1E1J), [1E1P](https://www.rcsb.org/structure/1E1P), [1E1S](https://www.rcsb.org/structure/1E1S), [1E1U](https://www.rcsb.org/structure/1E1U), [1E1W](https://www.rcsb.org/structure/1E1W) — incl. mutant structure 1E1G.

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

*Describes the biological roles of PRNP (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:** PRNP's established molecular role includes amyloid-beta binding. p.Pro60= falls in the disordered region.


### Pathways affected {#pathways}

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

| Pathway (Reactome) | Evidence |
| --- | --- |
| [Insertion of tail-anchored proteins into the endoplasmic reticulum membrane](https://reactome.org/content/detail/R-HSA-9609523) | electronic |
| [NCAM1 interactions](https://reactome.org/content/detail/R-HSA-419037) | electronic |

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

**Molecular function:** amyloid-beta binding, copper ion binding, microtubule binding, tubulin binding, identical protein binding, protein-containing complex binding.

**Biological process:** protein destabilization, intracellular signal transduction, positive regulation of neuron apoptotic process, positive regulation of calcium-mediated signaling, cellular response to copper ion, positive regulation of glutamate receptor signaling pathway.

## Clinical significance {#significance}

**Uncertain significance** — review status Single submitter *(criteria provided, single submitter)*, last evaluated 2016-06-26.

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

### Submitter classifications {#submitters}

| Submitter | Classification | Review | Method | Date |
| --- | --- | --- | --- | --- |
| Undiagnosed Diseases Network, NIH | Uncertain significance | criteria provided, single submitter | clinical testing | 2016-06-26 |

## Associated conditions {#conditions}

[spongiform encephalopathy with neuropsychiatric features](https://sugi.bio/atlas/disease/spongiform-encephalopathy-with-neuropsychiatric-features/).

**Reported phenotype names (ClinVar):** Spongiform encephalopathy with neuropsychiatric features.

## Similar variants {#similar}

Related PRNP variant pages (same residue, condition, or type): [PRNP p.Asp178Asn](/variant/prnp-p-asp178asn), [PRNP p.Glu200Lys](/variant/prnp-p-glu200lys), [PRNP p.Pro102Leu](/variant/prnp-p-pro102leu), [PRNP p.Thr183Ala](/variant/prnp-p-thr183ala), [PRNP c.*115G>A](/variant/prnp-c-star-115g-a), [PRNP p.Met166Ile](/variant/prnp-p-met166ile), [PRNP p.Met232Arg](/variant/prnp-p-met232arg), [PRNP p.Asn171Ser](/variant/prnp-p-asn171ser).

### Data sources & attribution {#sources}

ClinVar (NCBI — public domain, built 2026-10-14); gnomAD v4.1 (Broad Institute, built 2026-10-15); 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 453305). 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.*