Is PLAAT5 p.Ser52Pro (c.154T>C) pathogenic?

PLAAT5 p.Ser52Pro (c.154T>C) is classified Uncertain significance in PLAAT5 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-08-31). AlphaMissense: likely benign (0.0842); Absent from gnomAD v4.1.

How common is PLAAT5 p.Ser52Pro (c.154T>C) in the general population?

PLAAT5 p.Ser52Pro (c.154T>C) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about PLAAT5 p.Ser52Pro (c.154T>C)?

AlphaMissense predicts likely benign (score 0.0842) — an in-silico prediction, not a clinical call.

PLAAT5 p.Ser52Pro

c.154T>C · VCV4138445

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0842 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.0842	likely benign
REVEL	0.031	moderately benign-leaning
SaProt	LLR -5.80	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 -0.003	GERP -3.2
Regional constraint	o/e 1.07	unconstrained · MANE · 28 kb · p 0.19 · regional, not allelic
Overall
CADD	15.46	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.

⚠ Isoform check: AlphaMissense numbered on a different transcript (AM S62P vs ClinVar S52P) — verify the residue.

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: PLAAT5
Protein: p.Ser52Pro
Coding: c.154T>C
MANE Select: NM_001146729
Type: single nucleotide variant
Location: chr11:63490328 (GRCh38)
Gene constraint: LOEUF 1.612 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 62.39

Full PLAAT5 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

PLAAT5 p.Ala243Asp Uncertain significance ★ ⚠ same type
PLAAT5 p.Ala257Gly Uncertain significance ★ ⚠ same type
PLAAT5 p.Arg14His Uncertain significance ★ ⚠ same type
PLAAT5 p.Arg14Ser Uncertain significance ★ ⚠ same type
PLAAT5 p.Arg167Gln Uncertain significance ★ ⚠ same type
PLAAT5 p.Arg167Trp Uncertain significance ★ ⚠ same type
PLAAT5 p.Arg17Gly Uncertain significance ★ ⚠ same type
PLAAT5 p.Arg236Gln 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/plaat5-p-ser52pro (accessed [today's date]).

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