Is CHRDL1 p.Arg201Lys (c.602G>A) pathogenic?

CHRDL1 p.Arg201Lys (c.602G>A) is classified Uncertain significance in CHRDL1 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-03-16). AlphaMissense: likely pathogenic (0.5903); Absent from gnomAD v4.1; Associated with Inborn genetic diseases.

What condition is associated with CHRDL1 p.Arg201Lys (c.602G>A)?

CHRDL1 p.Arg201Lys (c.602G>A) is associated with Inborn genetic diseases (ClinVar).

How common is CHRDL1 p.Arg201Lys (c.602G>A) in the general population?

CHRDL1 p.Arg201Lys (c.602G>A) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about CHRDL1 p.Arg201Lys (c.602G>A)?

AlphaMissense predicts likely pathogenic (score 0.5903) — an in-silico prediction, not a clinical call.

CHRDL1 p.Arg201Lys

c.602G>A · VCV3267127

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.5903 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

1/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.5903	likely pathogenic
REVEL	0.162	moderately benign-leaning
SaProt	LLR -7.25	tolerated
⇒ AlphaMissense calls this damaging; REVEL and SaProt do not.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 7.1	GERP 1.6, phastCons 1
Regional constraint	o/e 0.93	unconstrained · MANE · 116 kb · p 0.22 · regional, not allelic
Overall
CADD	25.5	PHRED · no single calibrated threshold — expert panels disagree

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

⚠ Isoform check: AlphaMissense numbered on a different transcript (AM R200K vs ClinVar R201K) — verify the residue.

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: CHRDL1
Protein: p.Arg201Lys
Coding: c.602G>A
MANE Select: NM_001143981
Type: single nucleotide variant
Location: chrX:110700661 (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 p.Gln197= Benign/Likely benign ★★ 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.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-arg201lys (accessed [today's date]).

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