Is CDAN1 p.Ser79= (c.237G>C) pathogenic?

CDAN1 p.Ser79= (c.237G>C) is classified Benign/Likely benign in CDAN1 (ClinVar, Multiple submitters, 7 submitters; last evaluated 2026-01-22). Rare (popmax 0.766%, nfe); Associated with congenital dyserythropoietic anemia type 1.

What condition is associated with CDAN1 p.Ser79= (c.237G>C)?

CDAN1 p.Ser79= (c.237G>C) is associated with congenital dyserythropoietic anemia type 1, anemia, congenital dyserythropoietic, type 1a (ClinVar).

How common is CDAN1 p.Ser79= (c.237G>C) in the general population?

CDAN1 p.Ser79= (c.237G>C) is rare (popmax 0.766%, nfe) (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.Ser79=

c.237G>C · rs180857061 · VCV315955

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 7 submitters

gnomAD v4.1

Rare

rare (popmax 0.766%, nfe)

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 -0.83	GERP -2.8, phastCons 0.005
Overall
CADD	11.66	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.766% European (non-Finnish) · 8,676/1,132,426 alleles

Filtering AF 0.753% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.747%

Overall 0.629% 9,535/1,515,716 alleles · rare

Ancestry group	Frequency	1 in
Amishnot grpmax-eligible	2.52%	40
European (non-Finnish)grpmax	0.766%	131
Remaining individualsnot grpmax-eligible	0.539%	186
Admixed American	0.28%	357
South Asian	0.276%	362
Ashkenazi Jewishnot grpmax-eligible	0.175%	570
African / African-American	0.0922%	1,084
Finnishnot grpmax-eligible	0.0887%	1,128
Middle Eastern	0.0518%	1,930
East Asian	0.0027%	36,976

Amish shows a higher raw frequency than the grpmax group above it. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and “Remaining individuals” — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.

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.Ser79=
Coding: c.237G>C
MANE Select: NM_138477
dbSNP: rs180857061
Type: single nucleotide variant
Location: chr15:42736634 (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 79: the 'disordered' region

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

Also linked: anemia, congenital dyserythropoietic, type 1a

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.Ser79Leu Uncertain significance ★ ⚠ same residue
CDAN1 p.Arg1042Trp Pathogenic/Likely pathogenic ★★ ⚠ same condition
CDAN1 p.Arg682Ter 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

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-ser79 (accessed [today's date]).

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