Is CHRDL1 p.Gln197= (c.591A>G) pathogenic?

CHRDL1 p.Gln197= (c.591A>G) is classified Benign/Likely benign in CHRDL1 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2024-12-31). Rare (popmax 0.264%, afr); Associated with Inborn genetic diseases.

What condition is associated with CHRDL1 p.Gln197= (c.591A>G)?

CHRDL1 p.Gln197= (c.591A>G) is associated with Inborn genetic diseases (ClinVar).

How common is CHRDL1 p.Gln197= (c.591A>G) in the general population?

CHRDL1 p.Gln197= (c.591A>G) is rare (popmax 0.264%, afr) (gnomAD).

CHRDL1 p.Gln197=

c.591A>G · rs138473507 · VCV724378

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

rare (popmax 0.264%, afr)

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 · no allele here is in the release
Constraint at this position
Conservation	phyloP -8.1	GERP -3.1
Overall
CADD	0.207	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.264% African / African-American · 150/56,722 alleles

Filtering AF 0.23% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.217%

Overall 0.0172% 204/1,187,783 alleles · rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.264%	378
East Asian	0.0653%	1,531
Middle Eastern	0.0233%	4,290
Remaining individualsnot grpmax-eligible	0.0213%	4,688
South Asian	0.0107%	9,386
Admixed American	0.00438%	22,850
European (non-Finnish)	0.00149%	67,311

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: CHRDL1
Protein: p.Gln197=
Coding: c.591A>G
MANE Select: NM_001143981
dbSNP: rs138473507
Type: single nucleotide variant
Location: chrX:110700672 (GRCh38)
Structure: AlphaFold pLDDT 69.79

Full CHRDL1 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

CHRDL1 p.Glu423Asp Uncertain significance ★★ ⚠ same condition
CHRDL1 c.542-8A>G Conflicting classifications of pathogenicity ★ same condition
CHRDL1 p.Ala229Val Uncertain significance ★ ⚠ same condition
CHRDL1 p.Arg196Gln Conflicting classifications of pathogenicity ★ ⚠ same condition
CHRDL1 p.Arg196Trp Uncertain significance ★ ⚠ same condition
CHRDL1 p.Arg201Lys Uncertain significance ★ ⚠ same condition
CHRDL1 p.Arg209Cys Uncertain significance ★ ⚠ same condition
CHRDL1 p.Arg233Trp 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/chrdl1-p-gln197 (accessed [today's date]).

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