Is CDAN1 p.Val19= (c.57G>C) pathogenic?

CDAN1 p.Val19= (c.57G>C) is classified Conflicting classifications of pathogenicity in CDAN1 (ClinVar, Conflicting submitters, 2 submitters; last evaluated 2024-10-25). Ultra-rare (popmax 0.0895%, afr); Associated with congenital dyserythropoietic anemia type 1.

What condition is associated with CDAN1 p.Val19= (c.57G>C)?

CDAN1 p.Val19= (c.57G>C) is associated with congenital dyserythropoietic anemia type 1 (ClinVar).

How common is CDAN1 p.Val19= (c.57G>C) in the general population?

CDAN1 p.Val19= (c.57G>C) is ultra-rare (popmax 0.0895%, afr) (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.Val19=

c.57G>C · rs150418267 · VCV315957

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 0.0895%, afr)

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 3.8	GERP -0.38, phastCons 1
Overall
CADD	10.29	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0895% African / African-American · 65/72,610 alleles

Filtering AF 0.072% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0657%

Overall 0.00478% 74/1,548,102 alleles · ultra-rare exomes 33/1,395,984 · genomes 41/152,118 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.0895%	1,117
Middle Eastern	0.0168%	5,946
Admixed American	0.00777%	12,869
Remaining individualsnot grpmax-eligible	0.0067%	14,928

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.Val19=
Coding: c.57G>C
MANE Select: NM_138477
dbSNP: rs150418267
Type: single nucleotide variant
Location: chr15:42737046 (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 19: an α-helix

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-val19 (accessed [today's date]).

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