Is CDA p.Ile96Val (c.286A>G) pathogenic?

CDA p.Ile96Val (c.286A>G) is classified Uncertain significance in CDA (ClinVar, Single submitter, 1 submitter; last evaluated 2021-08-12). AlphaMissense: likely benign (0.1219); Rare (popmax 0.143%, sas).

How common is CDA p.Ile96Val (c.286A>G) in the general population?

CDA p.Ile96Val (c.286A>G) is rare (popmax 0.143%, sas) (gnomAD).

What do computational predictors say about CDA p.Ile96Val (c.286A>G)?

AlphaMissense predicts likely benign (score 0.1219) — an in-silico prediction, not a clinical call.

CDA p.Ile96Val

c.286A>G · rs549266010 · VCV2391428

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1219 · ACMG-weighted

gnomAD v4.1

Rare

rare (popmax 0.143%, sas)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.1219	likely benign
REVEL	0.064	moderately benign-leaning
SaProt	LLR -6.62	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 6.1	GERP 1.2, phastCons 1
Regional constraint	o/e 0.87	unconstrained · MANE · 29 kb · p 0.079 · regional, not allelic
Overall
CADD	21.9	PHRED · no single calibrated threshold — expert panels disagree

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

Grpmax group 0.143% South Asian · 130/91,070 alleles

Filtering AF 0.123% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.115%

Overall 0.00855% 138/1,614,042 alleles · rare

Ancestry group	Frequency	1 in
South Asiangrpmax	0.143%	701
Remaining individualsnot grpmax-eligible	0.0112%	8,928
European (non-Finnish)	8.47e-05%	1,179,947

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: CDA
Protein: p.Ile96Val
Coding: c.286A>G
MANE Select: NM_001785
dbSNP: rs549266010
Type: single nucleotide variant
Location: chr1:20613861 (GRCh38)
Gene constraint: LOEUF 0.955 · pLI 0.08 (gnomAD)
Structure: AlphaFold pLDDT 94.06 · 1 PDB
Residue 96: the cmp/dcmp-type deaminase domain; an α-helix

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

Similar variants

CDA p.Pro61= Benign ★★ same type
CDA p.Gln92His Uncertain significance ★ ⚠ same type
CDA p.Gly39Ala Uncertain significance ★ ⚠ same type
CDA p.Ile87Leu Uncertain significance ★ ⚠ same type
CDA p.Met117Ile Uncertain significance ★ ⚠ same type
CDA p.Pro120Leu Uncertain significance ★ ⚠ same type
CDA p.Thr123Met Uncertain significance ★ ⚠ same type
CDA p.Thr128Met 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/cda-p-ile96val (accessed [today's date]).

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