Is CHD7 p.Pro1855Ser (c.5563C>T) pathogenic?

CHD7 p.Pro1855Ser (c.5563C>T) is classified Uncertain significance in CHD7 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-06-18). AlphaMissense: likely pathogenic (0.7157); Very rare (popmax 0.00352%, sas); Associated with CHD7-related disorder.

What condition is associated with CHD7 p.Pro1855Ser (c.5563C>T)?

CHD7 p.Pro1855Ser (c.5563C>T) is associated with CHD7-related disorder (ClinVar).

How common is CHD7 p.Pro1855Ser (c.5563C>T) in the general population?

CHD7 p.Pro1855Ser (c.5563C>T) is very rare (popmax 0.00352%, sas) (gnomAD).

What do computational predictors say about CHD7 p.Pro1855Ser (c.5563C>T)?

AlphaMissense predicts likely pathogenic (score 0.7157) — an in-silico prediction, not a clinical call.

CHD7 p.Pro1855Ser

c.5563C>T · rs563402803 · VCV2632679

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.7157 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00352%, sas)

Conditions

CHD7-related disorder

Computational evidence

Protein change
AlphaMissense	0.7157	likely pathogenic
REVEL	0.432	indeterminate
SaProt	—	not scored · why
Splicing
SpliceAI	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP 7.7	GERP 2, phastCons 1
Regional constraint	o/e 0.88	unconstrained · MANE · 17 kb · p 7.3e-05 · regional, not allelic
Overall
CADD	23.9	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL is an independent agreement signal.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00352% South Asian · 3/85,142 alleles

Filtering AF 0.000936% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00046%

Overall 0.000191% 3/1,574,490 alleles · very rare exomes 2/1,422,486 · genomes 1/152,004 · joint denominator

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: CHD7
Protein: p.Pro1855Ser
Coding: c.5563C>T
MANE Select: NM_017780
dbSNP: rs563402803
Type: single nucleotide variant
Location: chr8:60851060 (GRCh38)
Gene constraint: LOEUF 0.109 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Residue 1855: the 'disordered' region

Full CHD7 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

CHD7-related disorder

Similar variants

CHD7 p.Pro1855= Likely benign ★★ same residue
CHD7 c.2836-1G>A Pathogenic/Likely pathogenic ★★ same condition
CHD7 c.2958-3A>G Likely pathogenic ★★ same condition
CHD7 c.4185+1G>A Pathogenic ★★ same condition
CHD7 c.5210+1G>A Pathogenic/Likely pathogenic ★★ same condition
CHD7 c.5211-2A>G Pathogenic ★★ same condition
CHD7 p.Arg1219Ter Pathogenic ★★ same condition
CHD7 p.Arg1345His 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-pro1855ser (accessed [today's date]).

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