Is CDON p.Asn609Ser (c.1826A>G) pathogenic?

CDON p.Asn609Ser (c.1826A>G) is classified Conflicting classifications of pathogenicity in CDON (ClinVar, Conflicting submitters, 3 submitters; last evaluated 2025-11-25). AlphaMissense: likely benign (0.1432); Ultra-rare (popmax 0.0349%, nfe); Associated with Inborn genetic diseases.

What condition is associated with CDON p.Asn609Ser (c.1826A>G)?

CDON p.Asn609Ser (c.1826A>G) is associated with Inborn genetic diseases, holoprosencephaly 11 (ClinVar).

How common is CDON p.Asn609Ser (c.1826A>G) in the general population?

CDON p.Asn609Ser (c.1826A>G) is ultra-rare (popmax 0.0349%, nfe) (gnomAD).

What do computational predictors say about CDON p.Asn609Ser (c.1826A>G)?

AlphaMissense predicts likely benign (score 0.1432) — an in-silico prediction, not a clinical call.

CDON p.Asn609Ser

c.1826A>G · rs756054017 · VCV303511

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 3 submitters

AlphaMissense

likely benign

0.1432 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0349%, nfe)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.1432	likely benign
REVEL	0.251	benign-leaning
SaProt	LLR -4.90	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 6.2	GERP 2, phastCons 1
Regional constraint	o/e 0.93	unconstrained · MANE · 63 kb · p 0.0032 · regional, not allelic
Overall
CADD	22.5	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

Grpmax group 0.0349% European (non-Finnish) · 412/1,180,018 alleles

Filtering AF 0.0321% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.031%

Overall 0.0271% 438/1,613,774 alleles · ultra-rare

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.0349%	2,864
Remaining individualsnot grpmax-eligible	0.0176%	5,678
African / African-American	0.00934%	10,705
Admixed American	0.00667%	15,001
South Asian	0.00439%	22,769

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.Asn609Ser
Coding: c.1826A>G
MANE Select: NM_001378964
dbSNP: rs756054017
Type: single nucleotide variant
Location: chr11:126005784 (GRCh38)
Gene constraint: LOEUF 0.733 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 62.62 · 3 PDB
Residue 609: the fibronectin type-iii 1 domain

Full CDON 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

Also linked: holoprosencephaly 11

Similar variants

CDON c.3276+1G>T Uncertain significance ★★ same condition
CDON c.640+1G>A Uncertain significance ★★ same condition
CDON c.*1805A>G Uncertain significance ★★ same condition
CDON c.*1816C>T Uncertain significance ★★ same condition
CDON c.*2349A>C Uncertain significance ★★ same condition
CDON c.*2377T>C Uncertain significance ★★ same condition
CDON c.*2760A>G Uncertain significance ★★ same condition
CDON p.Ala1099Val 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-asn609ser (accessed [today's date]).

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