Is CDV3 p.Pro140Ser (c.418C>T) pathogenic?

CDV3 p.Pro140Ser (c.418C>T) is classified Uncertain significance in CDV3 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-08-30). AlphaMissense: likely pathogenic (0.9153); Absent from gnomAD v4.1.

How common is CDV3 p.Pro140Ser (c.418C>T) in the general population?

CDV3 p.Pro140Ser (c.418C>T) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about CDV3 p.Pro140Ser (c.418C>T)?

AlphaMissense predicts likely pathogenic (score 0.9153) — an in-silico prediction, not a clinical call.

CDV3 p.Pro140Ser

c.418C>T · VCV4224895

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.9153 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

1/2 damaging

AlphaMissense, SaProt · REVEL no call

Computational evidence

Protein change
AlphaMissense	0.9153	likely pathogenic
REVEL	0.406	indeterminate
SaProt	LLR -6.51	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 7.7	GERP 2.4, phastCons 1
Regional constraint	o/e 1.08	unconstrained · MANE · 13 kb · p 0.28 · regional, not allelic
Overall
CADD	26.2	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: CDV3
Protein: p.Pro140Ser
Coding: c.418C>T
MANE Select: NM_017548
Type: single nucleotide variant
Location: chr3:133584102 (GRCh38)
Gene constraint: LOEUF 1.96 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 61.82
Residue 140: 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-pro140ser (accessed [today's date]).

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