Is CHD3 p.Phe551fs (c.1652_1653del) pathogenic?

CHD3 p.Phe551fs (c.16521653del) is classified Pathogenic in CHD3 (ClinVar, Single submitter, 1 submitter; last evaluated 2021-01-28). Absent from gnomAD; Associated with Snijders Blok-Campeau syndrome.

What condition is associated with CHD3 p.Phe551fs (c.1652_1653del)?

CHD3 p.Phe551fs (c.1652_1653del) is associated with Snijders Blok-Campeau syndrome (ClinVar).

How common is CHD3 p.Phe551fs (c.1652_1653del) in the general population?

CHD3 p.Phe551fs (c.1652_1653del) is absent from gnomAD (gnomAD).

CHD3 p.Phe551fs

c.1652_1653del · rs2544842992 · VCV1804082

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

Snijders Blok-Campeau syndrome

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function in a LoF-intolerant gene
NMD	predicted	premature termination codon in exon 10 of 40
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 1.1	GERP -3.2, phastCons 1

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: CHD3
Protein: p.Phe551fs
Coding: c.1652_1653del
MANE Select: NM_001005273
dbSNP: rs2544842992
Type: Deletion
Location: chr17:7895486 (GRCh38)
Gene constraint: LOEUF 0.257 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 63.21
Residue 551: the chromo 1 domain; 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.Ala191fs Likely pathogenic ★ same condition
CHD3 p.Arg1381fs Likely pathogenic ★ same condition
CHD3 p.Glu519fs Likely pathogenic ★ same condition
CHD3 c.4357_4358+2del Conflicting classifications of pathogenicity ★ ⚠ same condition
CHD3 p.Asp1671fs Conflicting classifications of pathogenicity ★ ⚠ same condition
CHD3 p.Ile20fs Uncertain significance ★ same condition
CHD3 p.Pro710fs Uncertain significance ★ same condition
CHD3 c.4073-3_4078del 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-phe551fs (accessed [today's date]).

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