Is SET p.Thr167= (c.501G>A) pathogenic?

SET p.Thr167= (c.501G>A) is classified Likely benign in SET (ClinVar, Single submitter, 1 submitter; last evaluated 2022-06-01). Ultra-rare (popmax 0.0114%, nfe).

How common is SET p.Thr167= (c.501G>A) in the general population?

SET p.Thr167= (c.501G>A) is ultra-rare (popmax 0.0114%, nfe) (gnomAD).

SET p.Thr167=

c.501G>A · VCV4904856

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0114%, nfe)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 1.5	GERP -1.6, phastCons 1
Overall
CADD	12.02	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0114% European (non-Finnish) · 134/1,178,564 alleles

Filtering AF 0.00979% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00919%

Overall 0.00888% 143/1,610,182 alleles · ultra-rare

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.0114%	8,795
Remaining individualsnot grpmax-eligible	0.00642%	15,585
African / African-American	0.00401%	24,909
East Asian	0.00223%	44,846
Admixed American	0.0017%	58,984

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.Thr167=
Coding: c.501G>A
MANE Select: NM_003011
Type: single nucleotide variant
Location: chr9:128693646 (GRCh38)
Gene constraint: LOEUF 0.167 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 78.62 · 3 PDB
Residue 167: a β-strand; the 'earmuff domain' region; the 'disordered' region

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

Similar variants

SET p.Thr167Met Uncertain significance ★ ⚠ same residue
SET c.663+5G>C Pathogenic ★★ same type
SET p.His105Tyr Likely pathogenic ★★ same type
SET p.Asp224Asn Uncertain significance ★★ ⚠ same type
SET p.Asp260Glu Uncertain significance ★★ ⚠ same type
SET p.Glu261Asp Uncertain significance ★★ ⚠ same type
SET p.Phe189Cys Uncertain significance ★★ ⚠ same type
SET c.132-17C>T Benign ★★ 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/set-p-thr167 (accessed [today's date]).

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