Is CHD2 p.Val1009Met (c.3025G>A) pathogenic?

CHD2 p.Val1009Met (c.3025G>A) is classified Likely benign in CHD2 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-02-18). AlphaMissense: likely benign (0.0881); Absent from gnomAD v4.1; Associated with Inborn genetic diseases.

What condition is associated with CHD2 p.Val1009Met (c.3025G>A)?

CHD2 p.Val1009Met (c.3025G>A) is associated with Inborn genetic diseases (ClinVar).

How common is CHD2 p.Val1009Met (c.3025G>A) in the general population?

CHD2 p.Val1009Met (c.3025G>A) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about CHD2 p.Val1009Met (c.3025G>A)?

AlphaMissense predicts likely benign (score 0.0881) — an in-silico prediction, not a clinical call.

CHD2 p.Val1009Met

c.3025G>A · VCV3832777

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0881 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.0881	likely benign
REVEL	0.058	moderately benign-leaning
SaProt	LLR -8.30	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 9.8	GERP 2.9, phastCons 1
Regional constraint	o/e 0.48	unconstrained · MANE · 6,370 bp · p 7.8e-14 · regional, not allelic
Overall
CADD	23.6	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: CHD2
Protein: p.Val1009Met
Coding: c.3025G>A
MANE Select: NM_001271
Type: single nucleotide variant
Location: chr15:92981416 (GRCh38)
Gene constraint: LOEUF 0.174 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 60.81
Residue 1009: a UniProt-annotated variant site (in dee94); a UniProt-annotated variant site (found in a patient with progressive myoclonus epilepsy; uncertain significance)

Full CHD2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

CHD2 p.Val1009Leu Uncertain significance ★★ ⚠ same residue
CHD2 c.443+1G>A Pathogenic/Likely pathogenic ★★ same condition
CHD2 p.Ala879Val Pathogenic/Likely pathogenic ★★ ⚠ same condition
CHD2 p.Arg1152Trp Pathogenic/Likely pathogenic ★★ same condition
CHD2 p.Arg1637Ter Pathogenic ★★ same condition
CHD2 p.Arg1679Ter Pathogenic ★★ same condition
CHD2 p.Arg699Trp Pathogenic/Likely pathogenic ★★ same condition
CHD2 p.Arg804Ter Pathogenic ★★ 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/chd2-p-val1009met (accessed [today's date]).

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