Is SETD2 p.Pro2102= (c.6306A>G) pathogenic?

SETD2 p.Pro2102= (c.6306A>G) is classified Likely benign in SETD2 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-10-13). Ultra-rare (popmax 0.0648%, sas); Associated with Luscan-Lumish syndrome.

What condition is associated with SETD2 p.Pro2102= (c.6306A>G)?

SETD2 p.Pro2102= (c.6306A>G) is associated with Luscan-Lumish syndrome (ClinVar).

How common is SETD2 p.Pro2102= (c.6306A>G) in the general population?

SETD2 p.Pro2102= (c.6306A>G) is ultra-rare (popmax 0.0648%, sas) (gnomAD).

SETD2 p.Pro2102=

c.6306A>G · rs539146125 · VCV1647613

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0648%, sas)

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 0.51	GERP -0.55, phastCons 1
Overall
CADD	6.331	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0648% South Asian · 59/91,064 alleles

Filtering AF 0.0515% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0467%

Overall 0.00384% 62/1,613,688 alleles · ultra-rare exomes 57/1,461,362 · genomes 5/152,326 · joint denominator

Ancestry group	Frequency	1 in
South Asiangrpmax	0.0648%	1,543
Admixed American	0.00333%	30,001
African / African-American	0.00133%	75,002

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.Pro2102=
Coding: c.6306A>G
MANE Select: NM_014159
dbSNP: rs539146125
Type: single nucleotide variant
Location: chr3:47057478 (GRCh38)
Gene constraint: LOEUF 0.176 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 43.81 · 43 PDB
Residue 2102: a UniProt-annotated variant site (in aml; uncertain significance; somatic mutation); a UniProt-annotated variant site (in all; 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.Pro2102Gln Uncertain significance ★ ⚠ same residue
SETD2 p.Pro2102Leu Uncertain significance ★ ⚠ same residue
SETD2 p.Pro2102Ser 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

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-pro2102 (accessed [today's date]).

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