Is CDAN1 p.Ala956= (c.2868C>T) pathogenic?

CDAN1 p.Ala956= (c.2868C>T) is classified Conflicting classifications of pathogenicity in CDAN1 (ClinVar, Conflicting submitters, 7 submitters; last evaluated 2025-07-01). Rare (popmax 0.157%, amr); Associated with congenital dyserythropoietic anemia type 1.

What condition is associated with CDAN1 p.Ala956= (c.2868C>T)?

CDAN1 p.Ala956= (c.2868C>T) is associated with congenital dyserythropoietic anemia type 1 (ClinVar).

How common is CDAN1 p.Ala956= (c.2868C>T) in the general population?

CDAN1 p.Ala956= (c.2868C>T) is rare (popmax 0.157%, amr) (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.Ala956=

c.2868C>T · rs150438471 · VCV315927

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 7 submitters

gnomAD v4.1

Rare

rare (popmax 0.157%, amr)

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	<0.2	all four deltas below 0.2 · G>C here scores Δ0.62 · evaluated, not missing
Constraint at this position
Conservation	phyloP -3	GERP -4.4
Overall
CADD	0.75	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.157% Admixed American · 94/59,994 alleles

Filtering AF 0.131% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.122%

Overall 0.00936% 151/1,613,264 alleles · rare exomes 84/1,461,210 · genomes 67/152,054 · joint denominator

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.157%	638
Middle Eastern	0.0823%	1,215
Remaining individualsnot grpmax-eligible	0.0144%	6,940
South Asian	0.00439%	22,769
European (non-Finnish)	0.00322%	31,051
African / African-American	0.00134%	74,876

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.Ala956=
Coding: c.2868C>T
MANE Select: NM_138477
dbSNP: rs150438471
Type: single nucleotide variant
Location: chr15:42728204 (GRCh38)
Gene constraint: LOEUF 0.908 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 72.58 · 2 PDB

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.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
CDAN1 c.1860+5G>A 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/cdan1-p-ala956 (accessed [today's date]).

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