Is CHD7 p.Ser392Ala (c.1174T>G) pathogenic?

CHD7 p.Ser392Ala (c.1174T>G) is classified Uncertain significance in CHD7 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-03-17). AlphaMissense: likely benign (0.1196); Absent from gnomAD v4.1; Associated with Inborn genetic diseases.

What condition is associated with CHD7 p.Ser392Ala (c.1174T>G)?

CHD7 p.Ser392Ala (c.1174T>G) is associated with Inborn genetic diseases (ClinVar).

How common is CHD7 p.Ser392Ala (c.1174T>G) in the general population?

CHD7 p.Ser392Ala (c.1174T>G) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about CHD7 p.Ser392Ala (c.1174T>G)?

AlphaMissense predicts likely benign (score 0.1196) — an in-silico prediction, not a clinical call.

CHD7 p.Ser392Ala

c.1174T>G · VCV4002169

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1196 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

0/2 damaging

AlphaMissense, REVEL · SaProt no call

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.1196	likely benign
REVEL	0.202	benign-leaning
SaProt	—	not scored · why
⇒ AlphaMissense and REVEL both call this tolerated; SaProt makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 7.9	GERP 2.6, phastCons 1
Regional constraint	o/e 0.99	unconstrained · MANE · 60 kb · p 0.84 · regional, not allelic
Overall
CADD	23.6	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 is an independent agreement signal.

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: CHD7
Protein: p.Ser392Ala
Coding: c.1174T>G
MANE Select: NM_017780
Type: single nucleotide variant
Location: chr8:60742606 (GRCh38)
Gene constraint: LOEUF 0.109 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Residue 392: the 'disordered' region

Full CHD7 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

CHD7 p.Ser392Phe Benign/Likely benign ★★ same residue
CHD7 p.Arg1494Ter Pathogenic ★★ same condition
CHD7 p.Arg157Ter Pathogenic ★★ same condition
CHD7 p.Arg2024Ter Pathogenic ★★ same condition
CHD7 p.Arg2098Ter Pathogenic ★★ same condition
CHD7 p.Arg2428Ter Pathogenic ★★ same condition
CHD7 p.Arg312Ter Pathogenic ★★ same condition
CHD7 p.Cys1101Tyr 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/chd7-p-ser392ala (accessed [today's date]).

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