Is CHD3 p.Arg1759Trp (c.5275C>T) pathogenic?

CHD3 p.Arg1759Trp (c.5275C>T) is classified Conflicting classifications of pathogenicity in CHD3 (ClinVar, Conflicting submitters, 4 submitters; last evaluated 2025-01-24). AlphaMissense: likely pathogenic (0.9991); Absent from gnomAD v4.1; Associated with Snijders Blok-Campeau syndrome.

What condition is associated with CHD3 p.Arg1759Trp (c.5275C>T)?

CHD3 p.Arg1759Trp (c.5275C>T) is associated with Snijders Blok-Campeau syndrome (ClinVar).

How common is CHD3 p.Arg1759Trp (c.5275C>T) in the general population?

CHD3 p.Arg1759Trp (c.5275C>T) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about CHD3 p.Arg1759Trp (c.5275C>T)?

AlphaMissense predicts likely pathogenic (score 0.9991) — an in-silico prediction, not a clinical call.

CHD3 p.Arg1759Trp

c.5275C>T · rs1394994913 · VCV2442106

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 4 submitters

AlphaMissense

likely pathogenic

0.9991 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

3/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Snijders Blok-Campeau syndrome

Computational evidence

Protein change
AlphaMissense	0.9991	likely pathogenic · top 4% in CHD3
REVEL	0.866	moderately pathogenic-leaning
SaProt	LLR -16.14	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 6	GERP 1.7, phastCons 1
Regional constraint	o/e 0.51	unconstrained · MANE · 732 bp · p 4.1e-05 · regional, not allelic
Overall
CADD	33.0	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: CHD3
Protein: p.Arg1759Trp
Coding: c.5275C>T
MANE Select: NM_001005273
dbSNP: rs1394994913
Type: single nucleotide variant
Location: chr17:7908710 (GRCh38)
Gene constraint: LOEUF 0.257 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 63.21
Residue 1759: the 'required for interaction with pcnt' region; a UniProt-annotated variant site (in snibcps)

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

Disease context

Snijders Blok-Campeau syndrome — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

CHD3 p.Arg1759Gln Likely pathogenic ★ same residue
CHD3 c.4073-2A>C Likely pathogenic ★★ same condition
CHD3 p.Arg1078Gln Pathogenic/Likely pathogenic ★★ same condition
CHD3 p.Arg1121Pro Pathogenic/Likely pathogenic ★★ same condition
CHD3 p.Arg1169Gln Pathogenic/Likely pathogenic ★★ same condition
CHD3 p.Arg1169Pro Pathogenic/Likely pathogenic ★★ same condition
CHD3 p.Arg1169Trp Pathogenic ★★ same condition
CHD3 p.Arg1172Gln Pathogenic/Likely 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/chd3-p-arg1759trp (accessed [today's date]).

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