Is CDADC1 p.Ser456Phe (c.1367C>T) pathogenic?

CDADC1 p.Ser456Phe (c.1367C>T) is classified Uncertain significance in CDADC1 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-11-08). AlphaMissense: likely pathogenic (0.978); Absent from gnomAD v4.1.

How common is CDADC1 p.Ser456Phe (c.1367C>T) in the general population?

CDADC1 p.Ser456Phe (c.1367C>T) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about CDADC1 p.Ser456Phe (c.1367C>T)?

AlphaMissense predicts likely pathogenic (score 0.978) — an in-silico prediction, not a clinical call.

CDADC1 p.Ser456Phe

c.1367C>T · rs2547073598 · VCV2324005

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.978 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

2/2 damaging

AlphaMissense, SaProt · REVEL no call

Computational evidence

Protein change
AlphaMissense	0.978	likely pathogenic · top 8% in CDADC1
REVEL	0.455	indeterminate
SaProt	LLR -10.06	damaging
⇒ AlphaMissense and SaProt both call this damaging; REVEL makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 7.6	GERP 2, phastCons 1
Regional constraint	o/e 0.84	unconstrained · MANE · 44 kb · p 5.1e-05 · regional, not allelic
Overall
CADD	31.0	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean damaging — 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

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.Ser456Phe
Coding: c.1367C>T
MANE Select: NM_030911
dbSNP: rs2547073598
Type: single nucleotide variant
Location: chr13:49280655 (GRCh38)
Gene constraint: LOEUF 0.917 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 79.53 · 4 PDB
Residue 456: the cmp/dcmp-type deaminase 2 domain

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-ser456phe (accessed [today's date]).

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