Is CHD3 p.Arg1491His (c.4472G>A) pathogenic?

CHD3 p.Arg1491His (c.4472G>A) is classified Uncertain significance in CHD3 (ClinVar, Multiple submitters, 3 submitters; last evaluated 2025-04-30). AlphaMissense: likely pathogenic (0.9922); Absent from gnomAD v4.1; Associated with CHD3-related disorder.

What condition is associated with CHD3 p.Arg1491His (c.4472G>A)?

CHD3 p.Arg1491His (c.4472G>A) is associated with CHD3-related disorder (ClinVar).

How common is CHD3 p.Arg1491His (c.4472G>A) in the general population?

CHD3 p.Arg1491His (c.4472G>A) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about CHD3 p.Arg1491His (c.4472G>A)?

AlphaMissense predicts likely pathogenic (score 0.9922) — an in-silico prediction, not a clinical call.

CHD3 p.Arg1491His

c.4472G>A · rs2545079624 · VCV2637217

Uncertain significance Multiple submitters

Classification

Uncertain significance

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

AlphaMissense

likely pathogenic

0.9922 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

3/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

CHD3-related disorder

Computational evidence

Protein change
AlphaMissense	0.9922	likely pathogenic
REVEL	0.915	moderately pathogenic-leaning
SaProt	LLR -11.18	damaging
⇒ AlphaMissense, REVEL and SaProt all call this damaging.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 12	GERP 1.9, phastCons 1
Regional constraint	o/e 0.37	unconstrained · MANE · 3,550 bp · p 4.9e-38 · regional, not allelic
Overall
CADD	32.0	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean damaging — a triage signal, not a reclassification

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: CHD3
Protein: p.Arg1491His
Coding: c.4472G>A
MANE Select: NM_001005273
dbSNP: rs2545079624
Type: single nucleotide variant
Location: chr17:7906666 (GRCh38)
Gene constraint: LOEUF 0.257 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 63.21
Residue 1491: a UniProt-annotated variant site (in snibcps)

Full CHD3 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

CHD3-related disorder

Similar variants

CHD3 p.Arg1172Gln Pathogenic/Likely pathogenic ★★ same condition
CHD3 p.Arg1342Gln Pathogenic/Likely pathogenic ★★ same condition
CHD3 p.Arg985Gln Pathogenic ★★ same condition
CHD3 p.Arg684Ter Pathogenic ★ same condition
CHD3 p.Glu1653Ter Likely pathogenic ★ same condition
CHD3 p.Met1085Ile Likely pathogenic ★ same condition
CHD3 p.Ala1289Thr Conflicting classifications of pathogenicity ★ ⚠ same condition
CHD3 p.Arg1342Trp Conflicting classifications of pathogenicity ★ ⚠ 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/chd3-p-arg1491his (accessed [today's date]).

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