Is CDAN1 p.Pro185Ser (c.553C>T) pathogenic?

CDAN1 p.Pro185Ser (c.553C>T) is classified Uncertain significance in CDAN1 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2025-08-19). AlphaMissense: likely benign (0.0766); Ultra-rare (popmax 0.0717%, amr); Associated with anemia, congenital dyserythropoietic, type 1a.

What condition is associated with CDAN1 p.Pro185Ser (c.553C>T)?

CDAN1 p.Pro185Ser (c.553C>T) is associated with anemia, congenital dyserythropoietic, type 1a (ClinVar).

How common is CDAN1 p.Pro185Ser (c.553C>T) in the general population?

CDAN1 p.Pro185Ser (c.553C>T) is ultra-rare (popmax 0.0717%, amr) (gnomAD).

How is Congenital dyserythropoietic anemia type I inherited?

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

What do computational predictors say about CDAN1 p.Pro185Ser (c.553C>T)?

AlphaMissense predicts likely benign (score 0.0766) — an in-silico prediction, not a clinical call.

CDAN1 p.Pro185Ser

c.553C>T · rs777322588 · VCV1163375

Uncertain significance Multiple submitters

Classification

Uncertain significance

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

AlphaMissense

likely benign

0.0766 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0717%, amr)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

anemia, congenital dyserythropoietic, type 1a

Computational evidence

Protein change
AlphaMissense	0.0766	likely benign
REVEL	0.141	moderately benign-leaning
SaProt	LLR -6.01	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 2	GERP -1.1, phastCons 0.99
Regional constraint	o/e 1.15	unconstrained · MANE · 1,562 bp · p 0.0016 · regional, not allelic
Overall
CADD	10.21	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — a triage signal, not a reclassification

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0717% Admixed American · 43/60,006 alleles

Filtering AF 0.0546% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0486%

Overall 0.00347% 56/1,613,566 alleles · ultra-rare exomes 50/1,461,486 · genomes 6/152,080 · joint denominator

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.0717%	1,395
Remaining individualsnot grpmax-eligible	0.0016%	62,470
African / African-American	0.00134%	74,884
European (non-Finnish)	0.000932%	107,263

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.Pro185Ser
Coding: c.553C>T
MANE Select: NM_138477
dbSNP: rs777322588
Type: single nucleotide variant
Location: chr15:42736318 (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 185: the 'disordered' region

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)

Similar variants

CDAN1 p.Pro185= Likely benign ★ 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-pro185ser (accessed [today's date]).

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