Is CHD1 p.Ser705fs (c.2112dup) pathogenic?

CHD1 p.Ser705fs (c.2112dup) is classified Likely pathogenic in CHD1 (ClinVar, Single submitter, 1 submitter; last evaluated 2026-01-20). No gnomAD frequency available for this variant; Associated with Pilarowski-Bjornsson syndrome.

What condition is associated with CHD1 p.Ser705fs (c.2112dup)?

CHD1 p.Ser705fs (c.2112dup) is associated with Pilarowski-Bjornsson syndrome (ClinVar).

How common is CHD1 p.Ser705fs (c.2112dup) in the general population?

CHD1 p.Ser705fs (c.2112dup) is no gnomAD frequency available for this variant (gnomAD).

CHD1 p.Ser705fs

c.2112dup · rs772328348 · VCV3254730

Likely pathogenic Single submitter

Classification

Likely 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

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	predicted	premature termination codon in exon 15 of 36
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 11	GERP 1.9, 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: CHD1
Protein: p.Ser705fs
Coding: c.2112dup
MANE Select: NM_001270
dbSNP: rs772328348
Type: Duplication
Location: chr5:98892592 (GRCh38)
Gene constraint: LOEUF 0.207 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 62.63 · 18 PDB

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.Ser215fs Likely pathogenic ★ same condition
CHD1 c.4108-554dup 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
CHD1 p.Asn1518His Uncertain significance ★★ ⚠ same condition
CHD1 p.Asn557Lys Uncertain significance ★★ ⚠ same condition
CHD1 p.Asp221Val 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-ser705fs (accessed [today's date]).

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