Is CDV3 p.Asp17Asn (c.49G>A) pathogenic?

CDV3 p.Asp17Asn (c.49G>A) is classified Uncertain significance in CDV3 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-02-07). AlphaMissense: likely pathogenic (0.9953); Absent from gnomAD v4.1.

How common is CDV3 p.Asp17Asn (c.49G>A) in the general population?

CDV3 p.Asp17Asn (c.49G>A) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about CDV3 p.Asp17Asn (c.49G>A)?

AlphaMissense predicts likely pathogenic (score 0.9953) — an in-silico prediction, not a clinical call.

CDV3 p.Asp17Asn

c.49G>A · rs2529823112 · VCV2481476

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.9953 · ACMG-weighted

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,240,172)

Missense predictors

2/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.9953	likely pathogenic · top 4% in CDV3
REVEL	0.081	moderately benign-leaning
SaProt	LLR -10.18	damaging
⇒ AlphaMissense and SaProt call this damaging; REVEL does not.
Splicing
SpliceAI	<0.2	all four deltas below 0.2 · G>T here scores Δ0.85 · evaluated, not missing
Constraint at this position
Conservation	phyloP 8.6	GERP -0.94, phastCons 1
Regional constraint	o/e 1.08	unconstrained · MANE · 13 kb · p 0.28 · regional, not allelic
Overall
CADD	24.4	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

No allele count reported in gnomAD v4.1 (AN 1,240,172). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: CDV3
Protein: p.Asp17Asn
Coding: c.49G>A
MANE Select: NM_017548
dbSNP: rs2529823112
Type: single nucleotide variant
Location: chr3:133574093 (GRCh38)
Gene constraint: LOEUF 1.96 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 61.82
Residue 17: the 'disordered' region

Full CDV3 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CDV3 p.Ala145Gly Uncertain significance ★ ⚠ same type
CDV3 p.Ala149Val Uncertain significance ★ ⚠ same type
CDV3 p.Ala35Val Uncertain significance ★ ⚠ same type
CDV3 p.Ala52Val Uncertain significance ★ ⚠ same type
CDV3 p.Ala68Gly Uncertain significance ★ ⚠ same type
CDV3 p.Ala68Pro Uncertain significance ★ ⚠ same type
CDV3 p.Ala73Val Uncertain significance ★ ⚠ same type
CDV3 p.Arg117Gly 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/cdv3-p-asp17asn (accessed [today's date]).

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