Is CHD5 p.Ile802Phe (c.2404A>T) pathogenic?

CHD5 p.Ile802Phe (c.2404A>T) is classified Uncertain significance in CHD5 (ClinVar, Single submitter, 1 submitter; last evaluated 2021-08-18). AlphaMissense: likely benign (0.2856); Absent from gnomAD v4.1.

How common is CHD5 p.Ile802Phe (c.2404A>T) in the general population?

CHD5 p.Ile802Phe (c.2404A>T) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about CHD5 p.Ile802Phe (c.2404A>T)?

AlphaMissense predicts likely benign (score 0.2856) — an in-silico prediction, not a clinical call.

CHD5 p.Ile802Phe

c.2404A>T · rs2100857040 · VCV1440989

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.2856 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

0/2 damaging

AlphaMissense, SaProt · REVEL no call

Computational evidence

Protein change
AlphaMissense	0.2856	likely benign
REVEL	0.607	indeterminate
SaProt	LLR -9.09	tolerated
⇒ AlphaMissense and SaProt both call this tolerated; REVEL makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 1.9	GERP 1.1, phastCons 0.99
Overall
CADD	22.4	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — a triage signal, not a reclassification

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: CHD5
Protein: p.Ile802Phe
Coding: c.2404A>T
MANE Select: NM_015557
dbSNP: rs2100857040
Type: single nucleotide variant
Location: chr1:6142160 (GRCh38)
Structure: AlphaFold pLDDT 78.15 · 4 PDB

Full CHD5 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CHD5 p.Ile802Leu Uncertain significance ★ ⚠ same residue
CHD5 c.4171+1G>A Pathogenic/Likely pathogenic ★★ same type
CHD5 p.Arg1618Ter Pathogenic/Likely pathogenic ★★ same type
CHD5 p.Arg193Trp Pathogenic/Likely pathogenic ★★ same type
CHD5 p.Pro1124Leu Pathogenic/Likely pathogenic ★★ same type
CHD5 p.Ser912Phe Pathogenic/Likely pathogenic ★★ same type
CHD5 c.2043+4A>T Uncertain significance ★★ same type
CHD5 c.79+5G>A Uncertain significance ★★ same type

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/chd5-p-ile802phe (accessed [today's date]).

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