Is CDADC1 p.Arg300Cys (c.898C>T) pathogenic?

CDADC1 p.Arg300Cys (c.898C>T) is classified Likely benign in CDADC1 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-04-20). AlphaMissense: likely benign (0.0477); Ultra-rare (popmax 0.0691%, eas).

How common is CDADC1 p.Arg300Cys (c.898C>T) in the general population?

CDADC1 p.Arg300Cys (c.898C>T) is ultra-rare (popmax 0.0691%, eas) (gnomAD).

What do computational predictors say about CDADC1 p.Arg300Cys (c.898C>T)?

AlphaMissense predicts likely benign (score 0.0477) — an in-silico prediction, not a clinical call.

CDADC1 p.Arg300Cys

c.898C>T · VCV3998402

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0477 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0691%, eas)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.0477	likely benign
REVEL	0.071	moderately benign-leaning
SaProt	LLR -4.75	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 5.1	GERP 0.58, phastCons 1
Regional constraint	o/e 0.84	unconstrained · MANE · 44 kb · p 5.1e-05 · regional, not allelic
Overall
CADD	21.1	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

Grpmax group 0.0691% East Asian · 31/44,888 alleles

Filtering AF 0.05% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0435%

Overall 0.00304% 49/1,613,902 alleles · ultra-rare

Ancestry group	Frequency	1 in
East Asiangrpmax	0.0691%	1,448
Remaining individualsnot grpmax-eligible	0.0016%	62,486
European (non-Finnish)	0.00136%	73,748
South Asian	0.0011%	91,080

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: CDADC1
Protein: p.Arg300Cys
Coding: c.898C>T
MANE Select: NM_030911
Type: single nucleotide variant
Location: chr13:49267957 (GRCh38)
Gene constraint: LOEUF 0.917 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 79.53 · 4 PDB

Full CDADC1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CDADC1 p.Arg300His Uncertain significance ★ ⚠ same residue
CDADC1 p.Gly119Glu Uncertain significance ★★ ⚠ same type
CDADC1 p.Ala110Thr Uncertain significance ★ ⚠ same type
CDADC1 p.Arg17Pro Uncertain significance ★ ⚠ same type
CDADC1 p.Arg273Ser Uncertain significance ★ ⚠ same type
CDADC1 p.Arg332Gln Uncertain significance ★ ⚠ same type
CDADC1 p.Arg510His Uncertain significance ★ ⚠ same type
CDADC1 p.Asn247Ser Uncertain significance ★ ⚠ 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/cdadc1-p-arg300cys (accessed [today's date]).

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