Is SETD2 p.Thr468= (c.1404A>G) pathogenic?

SETD2 p.Thr468= (c.1404A>G) is classified Likely benign in SETD2 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-03-05). Ultra-rare (popmax 0.0349%, amr); Associated with Luscan-Lumish syndrome.

What condition is associated with SETD2 p.Thr468= (c.1404A>G)?

SETD2 p.Thr468= (c.1404A>G) is associated with Luscan-Lumish syndrome (ClinVar).

How common is SETD2 p.Thr468= (c.1404A>G) in the general population?

SETD2 p.Thr468= (c.1404A>G) is ultra-rare (popmax 0.0349%, amr) (gnomAD).

SETD2 p.Thr468=

c.1404A>G · rs368082274 · VCV1126243

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0349%, amr)

Conditions

Luscan-Lumish syndrome

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 -0.29	GERP -4.1, phastCons 0.33
Overall
CADD	6.237	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0349% Admixed American · 18/51,524 alleles

Filtering AF 0.0225% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0186%

Overall 0.00981% 153/1,559,106 alleles · ultra-rare exomes 139/1,406,878 · genomes 14/152,228 · joint denominator

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.0349%	2,862
European (non-Finnish)	0.0111%	8,985
African / African-American	0.00819%	12,207
Remaining individualsnot grpmax-eligible	0.00165%	60,442

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: SETD2
Protein: p.Thr468=
Coding: c.1404A>G
MANE Select: NM_014159
dbSNP: rs368082274
Type: single nucleotide variant
Location: chr3:47123232 (GRCh38)
Gene constraint: LOEUF 0.176 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 43.81 · 43 PDB
Residue 468: a UniProt-annotated variant site (in aml; uncertain significance; somatic mutation); the 'disordered' region

Full SETD2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Luscan-Lumish syndrome — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

SETD2 p.Thr468Ile Benign ★ same residue
SETD2 p.Arg1598Ter Pathogenic/Likely pathogenic ★★ same condition
SETD2 p.Arg1740Gln Pathogenic ★★ ⚠ same condition
SETD2 p.Arg1740Trp Pathogenic/Likely pathogenic ★★ same condition
SETD2 p.Ala1121Thr Uncertain significance ★★ ⚠ same condition
SETD2 p.Ala679Val Uncertain significance ★★ ⚠ same condition
SETD2 p.Arg1065Cys Uncertain significance ★★ same condition
SETD2 p.Arg329Gln Uncertain significance ★★ ⚠ same condition

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/setd2-p-thr468 (accessed [today's date]).

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