Is PRNP p.Gly20Ser (c.58G>A) pathogenic?

PRNP p.Gly20Ser (c.58G>A) is classified Uncertain significance in PRNP (ClinVar, Single submitter, 1 submitter; last evaluated 2021-07-27). AlphaMissense: likely benign (0.1107); Absent from gnomAD v4.1.

How common is PRNP p.Gly20Ser (c.58G>A) in the general population?

PRNP p.Gly20Ser (c.58G>A) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about PRNP p.Gly20Ser (c.58G>A)?

AlphaMissense predicts likely benign (score 0.1107) — an in-silico prediction, not a clinical call.

PRNP p.Gly20Ser

c.58G>A · VCV4944281

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1107 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

0/2 damaging

AlphaMissense, SaProt · REVEL no call

Computational evidence

Protein change
AlphaMissense	0.1107	likely benign
REVEL	0.552	indeterminate
SaProt	LLR -5.95	tolerated
⇒ AlphaMissense and SaProt both call this tolerated; REVEL makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 7.7	GERP 1.5, phastCons 1
Regional constraint	o/e 0.84	unconstrained · MANE · 758 bp · p 0.0025 · regional, not allelic
Overall
CADD	21.1	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — a triage signal, not a reclassification

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: PRNP
Protein: p.Gly20Ser
Coding: c.58G>A
MANE Select: NM_000311
Type: single nucleotide variant
Location: chr20:4699278 (GRCh38)
Gene constraint: LOEUF 1.036 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 68.18 · 70 PDB

Full PRNP gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

PRNP p.Ala117Val Pathogenic ★★ ⚠ same type
PRNP p.Arg148His Likely pathogenic ★★ ⚠ same type
PRNP p.Arg208His Pathogenic/Likely pathogenic ★★ ⚠ same type
PRNP p.Asp178Asn Pathogenic/Likely pathogenic ★★ ⚠ same type
PRNP p.Gln217Arg Likely pathogenic ★★ ⚠ same type
PRNP p.Glu200Lys Pathogenic ★★ ⚠ same type
PRNP p.Gly131Val Pathogenic/Likely pathogenic ★★ same type
PRNP p.Phe198Ser Pathogenic ★★ ⚠ same type

Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →

Cite Sugi Variant

Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/prnp-p-gly20ser (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown