Is CDON p.Ile608= (c.1824C>A) pathogenic?

CDON p.Ile608= (c.1824C>A) is classified Likely benign in CDON (ClinVar, No assertion criteria, 1 submitter; last evaluated 2023-02-13). Absent from gnomAD v4.1; Associated with CDON-related disorder.

What condition is associated with CDON p.Ile608= (c.1824C>A)?

CDON p.Ile608= (c.1824C>A) is associated with CDON-related disorder (ClinVar).

How common is CDON p.Ile608= (c.1824C>A) in the general population?

CDON p.Ile608= (c.1824C>A) is absent from gnomAD v4.1 (gnomAD).

CDON p.Ile608=

c.1824C>A · rs1203653471 · VCV3052645

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

CDON-related disorder

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.265	benign-leaning
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 6.7	GERP 0.094, phastCons 1
Overall
CADD	11.5	PHRED · no single calibrated threshold — expert panels disagree

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: CDON
Protein: p.Ile608=
Coding: c.1824C>A
MANE Select: NM_001378964
dbSNP: rs1203653471
Type: single nucleotide variant
Location: chr11:126005786 (GRCh38)
Gene constraint: LOEUF 0.733 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 62.62 · 3 PDB
Residue 608: the fibronectin type-iii 1 domain

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

Disease context

CDON-related disorder

Similar variants

CDON p.Arg783His Uncertain significance ★★ ⚠ same condition
CDON p.Ile407Thr Uncertain significance ★★ ⚠ same condition
CDON p.Arg1187His Conflicting classifications of pathogenicity ★ ⚠ same condition
CDON p.Asn1062Thr Uncertain significance ★ ⚠ same condition
CDON p.Asn523Ser Uncertain significance ★ ⚠ same condition
CDON p.Gly1068Glu Uncertain significance ★ ⚠ same condition
CDON p.Gly1072Arg Uncertain significance ★ ⚠ same condition
CDON p.Gly1169Ser 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/cdon-p-ile608 (accessed [today's date]).

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