Is CDADC1 p.Cys426Ser (c.1277G>C) pathogenic?

CDADC1 p.Cys426Ser (c.1277G>C) is classified Uncertain significance in CDADC1 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-12-04). AlphaMissense: likely pathogenic (0.9701); Absent from gnomAD v4.1.

How common is CDADC1 p.Cys426Ser (c.1277G>C) in the general population?

CDADC1 p.Cys426Ser (c.1277G>C) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about CDADC1 p.Cys426Ser (c.1277G>C)?

AlphaMissense predicts likely pathogenic (score 0.9701) — an in-silico prediction, not a clinical call.

CDADC1 p.Cys426Ser

c.1277G>C · VCV4650785

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.9701 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

2/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.9701	likely pathogenic · top 9% in CDADC1
REVEL	0.969	strongly pathogenic-leaning
SaProt	LLR -9.99	tolerated
⇒ AlphaMissense and REVEL call this damaging; SaProt does not.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 12	GERP 2, phastCons 1
Regional constraint	o/e 0.84	unconstrained · MANE · 44 kb · p 5.1e-05 · regional, not allelic
Overall
CADD	32.0	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

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: CDADC1
Protein: p.Cys426Ser
Coding: c.1277G>C
MANE Select: NM_030911
Type: single nucleotide variant
Location: chr13:49280565 (GRCh38)
Gene constraint: LOEUF 0.917 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 79.53 · 4 PDB
Residue 426: the cmp/dcmp-type deaminase 2 domain; a binding site

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

Similar variants

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.Arg300His 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-cys426ser (accessed [today's date]).

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