Is CHD3 p.Asp29Glu (c.87C>G) pathogenic?

CHD3 p.Asp29Glu (c.87C>G) is classified Uncertain significance in CHD3 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-01-03). Very rare (popmax 0.0054%, amr); Associated with Snijders Blok-Campeau syndrome.

What condition is associated with CHD3 p.Asp29Glu (c.87C>G)?

CHD3 p.Asp29Glu (c.87C>G) is associated with Snijders Blok-Campeau syndrome (ClinVar).

How common is CHD3 p.Asp29Glu (c.87C>G) in the general population?

CHD3 p.Asp29Glu (c.87C>G) is very rare (popmax 0.0054%, amr) (gnomAD).

CHD3 p.Asp29Glu

c.87C>G · VCV4078263

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.0054%, amr)

Conditions

Snijders Blok-Campeau syndrome

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.255	benign-leaning
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 3.5	GERP 0.3, phastCons 1
Overall
CADD	16.32	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0054% Admixed American · 2/37,022 alleles

Filtering AF 0.000895% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000335%

Overall 0.000263% 3/1,140,974 alleles · very rare

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.0054%	18,511
Ashkenazi Jewishnot grpmax-eligible	0.00481%	20,774

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: CHD3
Protein: p.Asp29Glu
Coding: c.87C>G
MANE Select: NM_001005273 · reported on NM_001005271
Type: single nucleotide variant
Location: chr17:7884893 (GRCh38)
Gene constraint: LOEUF 0.257 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 63.21
Residue 29: the 'disordered' region

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 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
CHD3 p.Arg1172Trp 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-asp29glu (accessed [today's date]).

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