Is SET p.Pro20Thr (c.58C>A) pathogenic?

SET p.Pro20Thr (c.58C>A) is classified Uncertain significance in SET (ClinVar, Single submitter, 1 submitter; last evaluated 2024-04-11). AlphaMissense: likely benign (0.0675); No allele count reported in gnomAD v4.1 (AN 1,557,694).

How common is SET p.Pro20Thr (c.58C>A) in the general population?

SET p.Pro20Thr (c.58C>A) is no allele count reported in gnomAD v4.1 (AN 1,557,694) (gnomAD).

What do computational predictors say about SET p.Pro20Thr (c.58C>A)?

AlphaMissense predicts likely benign (score 0.0675) — an in-silico prediction, not a clinical call.

SET p.Pro20Thr

c.58C>A · VCV3372463

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0675 · ACMG-weighted

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,557,694)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

⚠ Built without this gene's context — gene constraint and dosage, protein structure, pathways, panels and related-variant links were not looked up for this page. why

Computational evidence

Protein change
AlphaMissense	0.0675	likely benign
REVEL	0.091	moderately benign-leaning
SaProt	LLR -7.66	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP -0.58	GERP -4.8
Overall
CADD	0.412	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

No allele count reported in gnomAD v4.1 (AN 1,557,694). 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: SET
Protein: p.Pro20Thr
Coding: c.58C>A
MANE Select: NM_003011 · reported on NM_001122821
Type: single nucleotide variant
Location: chr9:128683953 (GRCh38)

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

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/set-p-pro20thr (accessed [today's date]).

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