Is CDAN1 p.Glu467Asp (c.1401A>C) pathogenic?

CDAN1 p.Glu467Asp (c.1401A>C) is classified Uncertain significance in CDAN1 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-08-11). AlphaMissense: ambiguous (0.5363); Ultra-rare (popmax 0.0579%, eas).

How common is CDAN1 p.Glu467Asp (c.1401A>C) in the general population?

CDAN1 p.Glu467Asp (c.1401A>C) is ultra-rare (popmax 0.0579%, eas) (gnomAD).

What do computational predictors say about CDAN1 p.Glu467Asp (c.1401A>C)?

AlphaMissense predicts ambiguous (score 0.5363) — an in-silico prediction, not a clinical call.

CDAN1 p.Glu467Asp

c.1401A>C · rs202001507 · VCV1903534

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

ambiguous

0.5363 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0579%, eas)

Missense predictors

1/2 damaging

REVEL, SaProt · AlphaMissense no call

Computational evidence

Protein change
AlphaMissense	0.5363	ambiguous
REVEL	0.698	pathogenic-leaning
SaProt	LLR -7.87	tolerated
⇒ REVEL calls this damaging; SaProt does not; AlphaMissense makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 3.5	GERP 1.2, phastCons 1
Regional constraint	o/e 0.79	unconstrained · MANE · 3,842 bp · p 0.0002 · regional, not allelic
Overall
CADD	23.8	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

Grpmax group 0.0579% East Asian · 26/44,886 alleles

Filtering AF 0.0405% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0347%

Overall 0.00161% 26/1,614,066 alleles · ultra-rare exomes 18/1,461,880 · genomes 8/152,186 · joint denominator

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.Glu467Asp
Coding: c.1401A>C
MANE Select: NM_138477
dbSNP: rs202001507
Type: single nucleotide variant
Location: chr15:42733153 (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 467: an α-helix

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

Similar variants

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CDAN1 p.Arg714Trp Pathogenic/Likely pathogenic ★★ ⚠ same type
CDAN1 p.Asn599Ser Likely pathogenic ★★ ⚠ same type
CDAN1 p.Phe52Leu Pathogenic/Likely pathogenic ★★ ⚠ same type
CDAN1 p.Pro1130Leu Pathogenic/Likely pathogenic ★★ same type
CDAN1 p.Pro51Leu Likely pathogenic ★★ ⚠ same type
CDAN1 p.Pro672Leu Pathogenic/Likely pathogenic ★★ ⚠ same type

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-glu467asp (accessed [today's date]).

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