Is SETD2 p.Asp1788= (c.5364C>T) pathogenic?

SETD2 p.Asp1788= (c.5364C>T) is classified Likely benign in SETD2 (ClinVar, Single submitter, 2 submitters; last evaluated 2020-04-26). Ultra-rare (popmax 0.0198%, sas); Associated with Luscan-Lumish syndrome.

What condition is associated with SETD2 p.Asp1788= (c.5364C>T)?

SETD2 p.Asp1788= (c.5364C>T) is associated with Luscan-Lumish syndrome (ClinVar).

How common is SETD2 p.Asp1788= (c.5364C>T) in the general population?

SETD2 p.Asp1788= (c.5364C>T) is ultra-rare (popmax 0.0198%, sas) (gnomAD).

SETD2 p.Asp1788=

c.5364C>T · rs148618471 · VCV542242

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

ultra-rare (popmax 0.0198%, sas)

Conditions

Luscan-Lumish syndrome

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	<0.2	all four deltas below 0.2 · G>C here scores Δ0.25 · evaluated, not missing
Constraint at this position
Conservation	phyloP 0.7	GERP -4, phastCons 0.97
Overall
CADD	9.077	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0198% South Asian · 18/91,074 alleles

Filtering AF 0.0127% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0106%

Overall 0.00998% 161/1,612,998 alleles · ultra-rare exomes 151/1,460,784 · genomes 10/152,214 · joint denominator

Ancestry group	Frequency	1 in
South Asiangrpmax	0.0198%	5,060
European (non-Finnish)	0.011%	9,071
Admixed American	0.00667%	14,991
Remaining individualsnot grpmax-eligible	0.00641%	15,608
East Asian	0.00446%	22,420
African / African-American	0.004%	24,990

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.Asp1788=
Coding: c.5364C>T
MANE Select: NM_014159
dbSNP: rs148618471
Type: single nucleotide variant
Location: chr3:47086228 (GRCh38)
Gene constraint: LOEUF 0.176 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 43.81 · 43 PDB
Residue 1788: 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-asp1788 (accessed [today's date]).

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