Is CHD8 p.Phe993del (c.2979_2981del) pathogenic?

CHD8 p.Phe993del (c.29792981del) is classified Uncertain significance in CHD8 (ClinVar, Single submitter, 1 submitter; last evaluated 2016-05-06). No gnomAD frequency available for this variant; Associated with Inborn genetic diseases.

What condition is associated with CHD8 p.Phe993del (c.2979_2981del)?

CHD8 p.Phe993del (c.2979_2981del) is associated with Inborn genetic diseases (ClinVar).

How common is CHD8 p.Phe993del (c.2979_2981del) in the general population?

CHD8 p.Phe993del (c.2979_2981del) is no gnomAD frequency available for this variant (gnomAD).

CHD8 p.Phe993del

c.2979_2981del · rs1555315345 · VCV521047

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

Inborn genetic diseases

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 0.024	GERP 0.91, phastCons 0.82

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: CHD8
Protein: p.Phe993del
Coding: c.2979_2981del
MANE Select: NM_001170629
dbSNP: rs1555315345
Type: Deletion
Location: chr14:21405791 (GRCh38)
Gene constraint: LOEUF 0.154 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 55.17 · 2 PDB
Residue 993: the helicase atp-binding domain

Full CHD8 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

CHD8 c.5051+1del Pathogenic ★ same condition
CHD8 c.5053delG Pathogenic ★ same condition
CHD8 p.Arg709fs Pathogenic ★ same condition
CHD8 p.Cys944fs Pathogenic ★ same condition
CHD8 c.844-8_844-4del Uncertain significance ★ same condition
CHD8 c.3882+1G>A Pathogenic/Likely pathogenic ★★ same condition
CHD8 p.Arg1462Ter Pathogenic ★★ same condition
CHD8 p.Arg1582Ter 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/chd8-p-phe993del (accessed [today's date]).

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