Is PLPP5 p.Arg87Lys (c.260G>A) pathogenic?

PLPP5 p.Arg87Lys (c.260G>A) is classified Likely benign in PLPP5 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-05-26). AlphaMissense: likely benign (0.0837); No allele count reported in gnomAD v4.1 (AN 1,569,024).

How common is PLPP5 p.Arg87Lys (c.260G>A) in the general population?

PLPP5 p.Arg87Lys (c.260G>A) is no allele count reported in gnomAD v4.1 (AN 1,569,024) (gnomAD).

What do computational predictors say about PLPP5 p.Arg87Lys (c.260G>A)?

AlphaMissense predicts likely benign (score 0.0837) — an in-silico prediction, not a clinical call.

PLPP5 p.Arg87Lys

c.260G>A · VCV3934627

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0837 · ACMG-weighted

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,569,024)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.0837	likely benign
REVEL	0.235	benign-leaning
SaProt	LLR -6.88	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -2.9	GERP -3.5
Regional constraint	o/e 0.95	unconstrained · MANE · 4,752 bp · p 0.35 · regional, not allelic
Overall
CADD	0.019	PHRED · no single calibrated threshold — expert panels disagree

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

Population frequency

gnomAD v4.1 · exomes + genomes

No allele count reported in gnomAD v4.1 (AN 1,569,024). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: PLPP5
Protein: p.Arg87Lys
Coding: c.260G>A
MANE Select: NM_001102559
Type: single nucleotide variant
Location: chr8:38268385 (GRCh38)
Gene constraint: LOEUF 1.825 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 91.84

Full PLPP5 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

PLPP5 p.Ala156Pro Uncertain significance ★ ⚠ same type
PLPP5 p.Ala22Val Uncertain significance ★ ⚠ same type
PLPP5 p.Ala4Glu Uncertain significance ★ ⚠ same type
PLPP5 p.Ala5Val Uncertain significance ★ ⚠ same type
PLPP5 p.Ala96Pro Uncertain significance ★ ⚠ same type
PLPP5 p.Ala98Thr Uncertain significance ★ ⚠ same type
PLPP5 p.Arg115Gly Uncertain significance ★ ⚠ same type
PLPP5 p.Arg121Leu Uncertain significance ★ ⚠ 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/plpp5-p-arg87lys (accessed [today's date]).

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