Is SETD2 p.Val930del (c.2786TAG[1]) pathogenic?

SETD2 p.Val930del (c.2786TAG[1]) is classified Uncertain significance in SETD2 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-05-29). Very rare (popmax 8.47e-05%, nfe); Associated with Luscan-Lumish syndrome.

What condition is associated with SETD2 p.Val930del (c.2786TAG[1])?

SETD2 p.Val930del (c.2786TAG[1]) is associated with Luscan-Lumish syndrome (ClinVar).

How common is SETD2 p.Val930del (c.2786TAG[1]) in the general population?

SETD2 p.Val930del (c.2786TAG[1]) is very rare (popmax 8.47e-05%, nfe) (gnomAD).

SETD2 p.Val930del

c.2786TAG[1] · VCV3699186

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 8.47e-05%, nfe)

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 · substitutions only
Constraint at this position
Conservation	phyloP 4.7	GERP 2.1, phastCons 1

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 8.47e-05% European (non-Finnish) · 1/1,180,002 alleles

Overall 6.2e-05% 1/1,614,082 alleles · very rare exomes 1/1,461,784 · genomes 0/152,298 · joint denominator

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.Val930del
Coding: c.2786TAG[1]
MANE Select: NM_014159
Type: Microsatellite
Location: chr3:47121845 (GRCh38)
Gene constraint: LOEUF 0.176 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 43.81 · 43 PDB
Residue 930: 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.Asp429_Ser430insTer Pathogenic/Likely pathogenic ★★ same condition
SETD2 p.Asp1841fs Likely pathogenic ★ same condition
SETD2 p.Leu1729_Ser1730insTer Pathogenic ★ same condition
SETD2 p.Val2282fs Pathogenic ★ same condition
SETD2 c.4917+3_4917+6del Uncertain significance ★ same condition
SETD2 p.Pro194_Pro196dup Uncertain significance ★ same condition
SETD2 c.7099-19GT[3] Likely benign ★ same condition
SETD2 p.Cys531del Likely benign ★ 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-val930del (accessed [today's date]).

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