Is CDAN1 p.Ala38= (c.114G>A) pathogenic?

CDAN1 p.Ala38= (c.114G>A) is classified Likely benign in CDAN1 (ClinVar, Multiple submitters, 3 submitters; last evaluated 2025-09-30). Rare (popmax 0.14%, eas); Associated with anemia, congenital dyserythropoietic, type 1a.

What condition is associated with CDAN1 p.Ala38= (c.114G>A)?

CDAN1 p.Ala38= (c.114G>A) is associated with anemia, congenital dyserythropoietic, type 1a (ClinVar).

How common is CDAN1 p.Ala38= (c.114G>A) in the general population?

CDAN1 p.Ala38= (c.114G>A) is rare (popmax 0.14%, 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.Ala38=

c.114G>A · rs560030704 · VCV1657090

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

gnomAD v4.1

Rare

rare (popmax 0.14%, eas)

Conditions

anemia, congenital dyserythropoietic, type 1a

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 -0.19	GERP -3.4, phastCons 0.007
Overall
CADD	9.545	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.14% East Asian · 55/39,190 alleles

Filtering AF 0.111% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.1%

Overall 0.00445% 69/1,551,610 alleles · rare

Ancestry group	Frequency	1 in
East Asiangrpmax	0.14%	713
Remaining individualsnot grpmax-eligible	0.0167%	6,002
South Asian	0.0024%	41,726
Admixed American	0.00193%	51,842
European (non-Finnish)	8.66e-05%	1,154,332

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.Ala38=
Coding: c.114G>A
MANE Select: NM_138477
dbSNP: rs560030704
Type: single nucleotide variant
Location: chr15:42736757 (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 38: an α-helix

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

Disease context

anemia, congenital dyserythropoietic, type 1a — 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)

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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-ala38 (accessed [today's date]).

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