Is CHD1 p.Phe1691fs (c.5073del) pathogenic?

CHD1 p.Phe1691fs (c.5073del) is classified Likely benign in CHD1 (ClinVar, Single submitter, 1 submitter; last evaluated 2026-04-18). Associated with Pilarowski-Bjornsson syndrome.

What condition is associated with CHD1 p.Phe1691fs (c.5073del)?

CHD1 p.Phe1691fs (c.5073del) is associated with Pilarowski-Bjornsson syndrome (ClinVar).

CHD1 p.Phe1691fs

c.5073del · VCV4851397

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Rare

Conditions

Pilarowski-Bjornsson 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	escapes	premature termination codon in the last exon (36 of 36) — the truncated protein is likely expressed. PVS1 input, not an applied code
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 7.7	GERP 1.9, phastCons 1

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

Variant & gene context

Gene: CHD1
Protein: p.Phe1691fs
Coding: c.5073del
MANE Select: NM_001270
Type: Deletion
Location: chr5:98856440 (GRCh38)
Gene constraint: LOEUF 0.207 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 62.63 · 18 PDB
Residue 1691: the 'disordered' region

Full CHD1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Pilarowski-Bjornsson syndrome — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

CHD1 p.His1499fs Pathogenic ★ same condition
CHD1 p.Pro368fs Likely pathogenic ★ same condition
CHD1 p.Ser164fs Likely pathogenic ★ same condition
CHD1 p.Lys1110_Pro1115del Uncertain significance ★ same condition
CHD1 p.Trp545fs Uncertain significance ★ same condition
CHD1 p.Arg1659Thr Uncertain significance ★★ ⚠ same condition
CHD1 p.Arg1708Gln Uncertain significance ★★ same condition
CHD1 p.Arg233His Uncertain significance ★★ 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/chd1-p-phe1691fs (accessed [today's date]).

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