Is CDON p.Ser1130Arg (c.3390C>G) pathogenic?

CDON p.Ser1130Arg (c.3390C>G) is classified Uncertain significance in CDON (ClinVar, Single submitter, 1 submitter; last evaluated 2023-07-29). AlphaMissense: likely pathogenic (0.7971); Absent from gnomAD v4.1; Associated with CDON-related disorder.

What condition is associated with CDON p.Ser1130Arg (c.3390C>G)?

CDON p.Ser1130Arg (c.3390C>G) is associated with CDON-related disorder (ClinVar).

How common is CDON p.Ser1130Arg (c.3390C>G) in the general population?

CDON p.Ser1130Arg (c.3390C>G) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about CDON p.Ser1130Arg (c.3390C>G)?

AlphaMissense predicts likely pathogenic (score 0.7971) — an in-silico prediction, not a clinical call.

CDON p.Ser1130Arg

c.3390C>G · rs1945658448 · VCV2631276

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.7971 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

1/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

CDON-related disorder

Computational evidence

Protein change
AlphaMissense	0.7971	likely pathogenic
REVEL	0.154	moderately benign-leaning
SaProt	LLR -7.72	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 4.3	GERP -0.98, phastCons 1
Regional constraint	o/e 0.93	unconstrained · MANE · 63 kb · p 0.0032 · regional, not allelic
Overall
CADD	19.66	PHRED · no single calibrated threshold — expert panels disagree

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

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.Ser1130Arg
Coding: c.3390C>G
MANE Select: NM_001378964
dbSNP: rs1945658448
Type: single nucleotide variant
Location: chr11:125961965 (GRCh38)
Gene constraint: LOEUF 0.733 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 62.62 · 3 PDB

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

Disease context

CDON-related disorder

Similar variants

CDON p.Ser1130Asn Uncertain significance ★ ⚠ same residue
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

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-ser1130arg (accessed [today's date]).

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