Is CDAN1 p.Ile802= (c.2406C>T) pathogenic?

CDAN1 p.Ile802= (c.2406C>T) is classified Conflicting classifications of pathogenicity in CDAN1 (ClinVar, Conflicting submitters, 2 submitters; last evaluated 2023-03-01). Ultra-rare (popmax 0.0446%, eas); Associated with congenital dyserythropoietic anemia type 1.

What condition is associated with CDAN1 p.Ile802= (c.2406C>T)?

CDAN1 p.Ile802= (c.2406C>T) is associated with congenital dyserythropoietic anemia type 1 (ClinVar).

How common is CDAN1 p.Ile802= (c.2406C>T) in the general population?

CDAN1 p.Ile802= (c.2406C>T) is ultra-rare (popmax 0.0446%, eas) (gnomAD).

How is Congenital dyserythropoietic anemia type I inherited?

Typically Autosomal recessive (Orphanet). A genetic counselor can assess individual risk for a family.

CDAN1 p.Ile802=

c.2406C>T · rs145050561 · VCV315935

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

ultra-rare (popmax 0.0446%, eas)

Conditions

congenital dyserythropoietic anemia type 1

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 -4.4	GERP -3.7
Overall
CADD	0.167	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0446% East Asian · 20/44,888 alleles

Filtering AF 0.0295% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0246%

Overall 0.00663% 107/1,614,168 alleles · ultra-rare exomes 98/1,461,864 · genomes 9/152,304 · joint denominator

Ancestry group	Frequency	1 in
East Asiangrpmax	0.0446%	2,244
South Asian	0.00988%	10,119
Admixed American	0.00666%	15,007
Remaining individualsnot grpmax-eligible	0.0064%	15,626
European (non-Finnish)	0.00559%	17,879
African / African-American	0.00533%	18,758

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: CDAN1
Protein: p.Ile802=
Coding: c.2406C>T
MANE Select: NM_138477
dbSNP: rs145050561
Type: single nucleotide variant
Location: chr15:42729569 (GRCh38)
Gene constraint: LOEUF 0.908 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 72.58 · 2 PDB
Residue 802: a turn

Full CDAN1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

congenital dyserythropoietic anemia type 1 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Congenital dyserythropoietic anemia type I (Orphanet):

Inheritance: Autosomal recessive
Onset: Adolescent, Adult, Childhood, Infancy, Neonatal
Prevalence: <1 / 1 000 000 (Europe)

Similar variants

CDAN1 p.Ile802Val Uncertain significance ★ ⚠ same residue
CDAN1 p.Arg1042Trp Pathogenic/Likely pathogenic ★★ ⚠ same condition
CDAN1 p.Arg714Trp Pathogenic/Likely pathogenic ★★ ⚠ same condition
CDAN1 p.Asn599Ser Likely pathogenic ★★ ⚠ same condition
CDAN1 p.Phe52Leu Pathogenic/Likely pathogenic ★★ ⚠ same condition
CDAN1 p.Pro1130Leu Pathogenic/Likely pathogenic ★★ same condition
CDAN1 p.Pro51Leu Likely pathogenic ★★ ⚠ same condition
CDAN1 p.Pro672Leu Pathogenic/Likely pathogenic ★★ ⚠ 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/cdan1-p-ile802 (accessed [today's date]).

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