Is CDADC1 p.Arg332Gln (c.995G>A) pathogenic?

CDADC1 p.Arg332Gln (c.995G>A) is classified Uncertain significance in CDADC1 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-07-17). AlphaMissense: likely pathogenic (0.6292); Ultra-rare (popmax 0.0165%, mid).

How common is CDADC1 p.Arg332Gln (c.995G>A) in the general population?

CDADC1 p.Arg332Gln (c.995G>A) is ultra-rare (popmax 0.0165%, mid) (gnomAD).

What do computational predictors say about CDADC1 p.Arg332Gln (c.995G>A)?

AlphaMissense predicts likely pathogenic (score 0.6292) — an in-silico prediction, not a clinical call.

CDADC1 p.Arg332Gln

c.995G>A · rs1247837567 · VCV2612307

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.6292 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0165%, mid)

Missense predictors

1/2 damaging

AlphaMissense, SaProt · REVEL no call

Computational evidence

Protein change
AlphaMissense	0.6292	likely pathogenic
REVEL	0.635	indeterminate
SaProt	LLR -6.78	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 12	GERP 1.8, phastCons 1
Regional constraint	o/e 0.84	unconstrained · MANE · 44 kb · p 5.1e-05 · regional, not allelic
Overall
CADD	27.9	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 0.0165% Middle Eastern · 1/6,048 alleles

Filtering AF 8e-05% ClinGen BA1/BS1 input FAF95, joint · FAF99 5.4e-05%

Overall 0.000481% 7/1,454,968 alleles · ultra-rare

Ancestry group	Frequency	1 in
Middle Easterngrpmax	0.0165%	6,048
Ashkenazi Jewishnot grpmax-eligible	0.00339%	29,492
African / African-American	0.00133%	74,948
European (non-Finnish)	0.00034%	294,377

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.Arg332Gln
Coding: c.995G>A
MANE Select: NM_030911
dbSNP: rs1247837567
Type: single nucleotide variant
Location: chr13:49268054 (GRCh38)
Gene constraint: LOEUF 0.917 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 79.53 · 4 PDB
Residue 332: 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.Arg510His Uncertain significance ★ ⚠ same type
CDADC1 p.Asn247Ser Uncertain significance ★ ⚠ same type
CDADC1 p.Cys137Gly 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-arg332gln (accessed [today's date]).

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