Is SETD2 p.Pro2419Arg (c.7256C>G) pathogenic?

SETD2 p.Pro2419Arg (c.7256C>G) is classified Uncertain significance in SETD2 (ClinVar, Single submitter, 1 submitter; last evaluated 2026-03-05). AlphaMissense: likely pathogenic (0.9869); Absent from gnomAD v4.1; Associated with intellectual developmental disorder, autosomal dominant 70.

What condition is associated with SETD2 p.Pro2419Arg (c.7256C>G)?

SETD2 p.Pro2419Arg (c.7256C>G) is associated with intellectual developmental disorder, autosomal dominant 70 (ClinVar).

How common is SETD2 p.Pro2419Arg (c.7256C>G) in the general population?

SETD2 p.Pro2419Arg (c.7256C>G) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about SETD2 p.Pro2419Arg (c.7256C>G)?

AlphaMissense predicts likely pathogenic (score 0.9869) — an in-silico prediction, not a clinical call.

SETD2 p.Pro2419Arg

c.7256C>G · VCV4813561

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.9869 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

1/2 damaging

AlphaMissense, SaProt · REVEL indeterminate

Conditions

intellectual developmental disorder, autosomal dominant 70

Computational evidence

Protein change
AlphaMissense	0.9869	likely pathogenic · top 8% in SETD2
REVEL	0.526	indeterminate
SaProt	LLR -5.46	tolerated
⇒ AlphaMissense calls this damaging; SaProt does not; REVEL is indeterminate.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 12	GERP 1.7, phastCons 1
Regional constraint	o/e 0.80	unconstrained · MANE · 19 kb · p 0.00059 · regional, not allelic
Overall
CADD	26.1	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: SETD2
Protein: p.Pro2419Arg
Coding: c.7256C>G
MANE Select: NM_014159
Type: single nucleotide variant
Location: chr3:47037760 (GRCh38)
Gene constraint: LOEUF 0.176 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 43.81 · 43 PDB
Residue 2419: a UniProt-annotated variant site (in aml; uncertain significance; somatic mutation); a UniProt-annotated variant site (in all; uncertain significance; somatic mutation); a β-strand; the ww domain

Full SETD2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

intellectual developmental disorder, autosomal dominant 70 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

SETD2 p.Arg1740Gln Pathogenic ★★ ⚠ same condition
SETD2 p.Arg1740Trp Pathogenic/Likely pathogenic ★★ same condition
SETD2 p.Arg401Gln Uncertain significance ★★ ⚠ same condition
SETD2 p.His266Tyr Uncertain significance ★★ ⚠ same condition
SETD2 p.Lys145Asn Uncertain significance ★★ ⚠ same condition
SETD2 p.Ser1207= Likely benign ★★ same condition
SETD2 p.Val1743Leu Likely pathogenic ★ ⚠ same condition
SETD2 c.4840-1G>A 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-pro2419arg (accessed [today's date]).

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