Is CDAN1 p.Arg97Ser (c.289C>A) pathogenic?

CDAN1 p.Arg97Ser (c.289C>A) is classified Uncertain significance in CDAN1 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-11-26). AlphaMissense: likely pathogenic (0.6179); No allele count reported in gnomAD v4.1 (AN 1,491,204); Associated with CDAN1-related disorder.

What condition is associated with CDAN1 p.Arg97Ser (c.289C>A)?

CDAN1 p.Arg97Ser (c.289C>A) is associated with CDAN1-related disorder (ClinVar).

How common is CDAN1 p.Arg97Ser (c.289C>A) in the general population?

CDAN1 p.Arg97Ser (c.289C>A) is no allele count reported in gnomAD v4.1 (AN 1,491,204) (gnomAD).

What do computational predictors say about CDAN1 p.Arg97Ser (c.289C>A)?

AlphaMissense predicts likely pathogenic (score 0.6179) — an in-silico prediction, not a clinical call.

CDAN1 p.Arg97Ser

c.289C>A · rs1286444553 · VCV2635130

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.6179 · ACMG-weighted

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,491,204)

Missense predictors

1/2 damaging

AlphaMissense, SaProt · REVEL no call

Conditions

CDAN1-related disorder

Computational evidence

Protein change
AlphaMissense	0.6179	likely pathogenic
REVEL	0.353	indeterminate
SaProt	LLR -6.30	tolerated
⇒ AlphaMissense calls this damaging; SaProt does not; REVEL makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 7.6	GERP -0.49, phastCons 1
Regional constraint	o/e 1.15	unconstrained · MANE · 1,562 bp · p 0.0016 · regional, not allelic
Overall
CADD	23.1	PHRED · no single calibrated threshold — expert panels disagree

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

Population frequency

gnomAD v4.1 · exomes + genomes

No allele count reported in gnomAD v4.1 (AN 1,491,204). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: CDAN1
Protein: p.Arg97Ser
Coding: c.289C>A
MANE Select: NM_138477
dbSNP: rs1286444553
Type: single nucleotide variant
Location: chr15:42736582 (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 97: the 'disordered' region

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

Disease context

CDAN1-related disorder

Similar variants

CDAN1 p.Arg97Cys Uncertain significance ★ same residue
CDAN1 p.Pro672Leu Pathogenic/Likely pathogenic ★★ ⚠ same condition
CDAN1 p.Arg934Trp Uncertain significance ★★ ⚠ same condition
CDAN1 c.1458-1G>A Likely pathogenic ★ same condition
CDAN1 p.Gln67Ter Likely pathogenic ★ same condition
CDAN1 p.Glu11Ter Likely pathogenic ★ same condition
CDAN1 p.Trp1184Ter Likely pathogenic ★ same condition
CDAN1 p.Arg677Trp Conflicting classifications of pathogenicity ★ ⚠ 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-arg97ser (accessed [today's date]).

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