Is SETD2 p.Gln1092= (c.3276A>G) pathogenic?

SETD2 p.Gln1092= (c.3276A>G) is classified Likely benign in SETD2 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2026-04-01). Ultra-rare (popmax 0.099%, mid); Associated with Luscan-Lumish syndrome.

What condition is associated with SETD2 p.Gln1092= (c.3276A>G)?

SETD2 p.Gln1092= (c.3276A>G) is associated with Luscan-Lumish syndrome (ClinVar).

How common is SETD2 p.Gln1092= (c.3276A>G) in the general population?

SETD2 p.Gln1092= (c.3276A>G) is ultra-rare (popmax 0.099%, mid) (gnomAD).

SETD2 p.Gln1092=

c.3276A>G · rs114327122 · VCV1145386

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

ultra-rare (popmax 0.099%, mid)

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 -11	GERP -4.6
Overall
CADD	0.075	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.099% Middle Eastern · 6/6,062 alleles

Filtering AF 0.043% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0294%

Overall 0.00863% 139/1,609,908 alleles · ultra-rare exomes 129/1,457,580 · genomes 10/152,328 · joint denominator

Ancestry group	Frequency	1 in
Middle Easterngrpmax	0.099%	1,010
European (non-Finnish)	0.0107%	9,365
Remaining individualsnot grpmax-eligible	0.0064%	15,619
Admixed American	0.005%	20,006

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.Gln1092=
Coding: c.3276A>G
MANE Select: NM_014159
dbSNP: rs114327122
Type: single nucleotide variant
Location: chr3:47121360 (GRCh38)
Gene constraint: LOEUF 0.176 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 43.81 · 43 PDB
Residue 1092: the 'disordered' region; a UniProt-annotated variant site (in aml; uncertain significance; somatic mutation); a UniProt-annotated variant site (in all; uncertain significance; somatic mutation)

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.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
SETD2 p.Arg368Gln 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-gln1092 (accessed [today's date]).

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