Is SET p.Pro10= (c.30G>A) pathogenic?

SET p.Pro10= (c.30G>A) is classified Likely benign in SET (ClinVar, Single submitter, 1 submitter; last evaluated 2018-04-24). Rare (popmax 0.135%, sas).

How common is SET p.Pro10= (c.30G>A) in the general population?

SET p.Pro10= (c.30G>A) is rare (popmax 0.135%, sas) (gnomAD).

SET p.Pro10=

c.30G>A · rs369353971 · VCV741914

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

rare (popmax 0.135%, sas)

⚠ 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
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP -1.2	GERP -5.5
Overall
CADD	7.232	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.135% South Asian · 114/84,168 alleles

Filtering AF 0.115% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.108%

Overall 0.0111% 173/1,555,110 alleles · rare exomes 153/1,402,922 · genomes 20/152,188 · joint denominator

Ancestry group	Frequency	1 in
South Asiangrpmax	0.135%	738
Remaining individualsnot grpmax-eligible	0.0132%	7,549
East Asian	0.00487%	20,545
African / African-American	0.0041%	24,401
European (non-Finnish)	0.004%	24,982

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: SET
Protein: p.Pro10=
Coding: c.30G>A
MANE Select: NM_003011 · reported on NM_001122821
dbSNP: rs369353971
Type: single nucleotide variant
Location: chr9:128683925 (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-pro10 (accessed [today's date]).

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