Is CHD5 p.Ala1855= (c.5565C>T) pathogenic?

CHD5 p.Ala1855= (c.5565C>T) is classified Likely benign in CHD5 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2024-06-18). Ultra-rare (popmax 0.0627%, afr); Associated with CHD5-related disorder.

What condition is associated with CHD5 p.Ala1855= (c.5565C>T)?

CHD5 p.Ala1855= (c.5565C>T) is associated with CHD5-related disorder (ClinVar).

How common is CHD5 p.Ala1855= (c.5565C>T) in the general population?

CHD5 p.Ala1855= (c.5565C>T) is ultra-rare (popmax 0.0627%, afr) (gnomAD).

CHD5 p.Ala1855=

c.5565C>T · VCV3350887

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0627%, afr)

Conditions

CHD5-related disorder

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -7.3	GERP -4
Overall
CADD	1.179	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0627% African / African-American · 47/75,014 alleles

Filtering AF 0.0483% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0433%

Overall 0.00471% 76/1,612,462 alleles · ultra-rare exomes 41/1,460,188 · genomes 35/152,274 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.0627%	1,596
Admixed American	0.0167%	5,996
Remaining individualsnot grpmax-eligible	0.0048%	20,813
European (non-Finnish)	0.00136%	73,722

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: CHD5
Protein: p.Ala1855=
Coding: c.5565C>T
MANE Select: NM_015557
Type: single nucleotide variant
Location: chr1:6109808 (GRCh38)
Structure: AlphaFold pLDDT 78.15 · 4 PDB

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

Disease context

CHD5-related disorder

Similar variants

CHD5 p.Asn1126Ser Uncertain significance ★★ ⚠ same condition
CHD5 p.Thr781Met Uncertain significance ★★ ⚠ same condition
CHD5 p.Gly976Cys Uncertain significance ★ ⚠ same condition
CHD5 p.Ile1735Asn Uncertain significance ★ ⚠ same condition
CHD5 p.Lys615Glu Uncertain significance ★ ⚠ same condition
CHD5 p.Thr340Ser Uncertain significance ★ ⚠ same condition
CHD5 p.Thr699Ser Uncertain significance ★ ⚠ same condition
CHD5 c.4540-6C>T 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/chd5-p-ala1855 (accessed [today's date]).

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