Is SETD2 p.Ser1353= (c.4059C>T) pathogenic?

SETD2 p.Ser1353= (c.4059C>T) is classified Benign/Likely benign in SETD2 (ClinVar, Multiple submitters, 4 submitters; last evaluated 2024-08-14). Rare (popmax 0.343%, afr); Associated with Luscan-Lumish syndrome.

What condition is associated with SETD2 p.Ser1353= (c.4059C>T)?

SETD2 p.Ser1353= (c.4059C>T) is associated with Luscan-Lumish syndrome (ClinVar).

How common is SETD2 p.Ser1353= (c.4059C>T) in the general population?

SETD2 p.Ser1353= (c.4059C>T) is rare (popmax 0.343%, afr) (gnomAD).

SETD2 p.Ser1353=

c.4059C>T · rs113560046 · VCV475516

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 4 submitters

gnomAD v4.1

Rare

rare (popmax 0.343%, afr)

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 0.52	GERP -0.43, phastCons 0.53
Overall
CADD	4.927	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.343% African / African-American · 257/75,006 alleles

Filtering AF 0.308% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.295%

Overall 0.0203% 327/1,614,020 alleles · rare exomes 174/1,461,814 · genomes 153/152,206 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.343%	292
East Asian	0.0245%	4,081
Remaining individualsnot grpmax-eligible	0.0224%	4,465
Admixed American	0.0217%	4,615
South Asian	0.00988%	10,119
Ashkenazi Jewishnot grpmax-eligible	0.00676%	14,802
European (non-Finnish)	0.00178%	56,191

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.Ser1353=
Coding: c.4059C>T
MANE Select: NM_014159
dbSNP: rs113560046
Type: single nucleotide variant
Location: chr3:47120577 (GRCh38)
Gene constraint: LOEUF 0.176 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 43.81 · 43 PDB
Residue 1353: 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.Ser1353Ala Uncertain significance ★ ⚠ 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-ser1353 (accessed [today's date]).

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