Is CDON p.Val737= (c.2211C>T) pathogenic?

CDON p.Val737= (c.2211C>T) is classified Likely benign in CDON (ClinVar, No assertion criteria, 1 submitter; last evaluated 2022-10-19). Very rare (popmax 0.000848%, nfe); Associated with CDON-related disorder.

What condition is associated with CDON p.Val737= (c.2211C>T)?

CDON p.Val737= (c.2211C>T) is associated with CDON-related disorder (ClinVar).

How common is CDON p.Val737= (c.2211C>T) in the general population?

CDON p.Val737= (c.2211C>T) is very rare (popmax 0.000848%, nfe) (gnomAD).

CDON p.Val737=

c.2211C>T · rs1484508740 · VCV3029514

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.000848%, nfe)

Conditions

CDON-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 2.3	GERP -2.6, phastCons 1
Overall
CADD	8.185	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.000848% European (non-Finnish) · 10/1,179,820 alleles

Filtering AF 0.000429% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000313%

Overall 0.000684% 10/1,461,566 alleles · very rare

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: CDON
Protein: p.Val737=
Coding: c.2211C>T
MANE Select: NM_001378964
dbSNP: rs1484508740
Type: single nucleotide variant
Location: chr11:125997358 (GRCh38)
Gene constraint: LOEUF 0.733 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 62.62 · 3 PDB
Residue 737: the fibronectin type-iii 2 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-val737 (accessed [today's date]).

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