Is CPD p.Pro1019Ser (c.3055C>T) pathogenic?

CPD p.Pro1019Ser (c.3055C>T) is classified Uncertain significance in CPD (ClinVar, Single submitter, 1 submitter; last evaluated 2024-01-04). AlphaMissense: likely benign (0.0968); Absent from gnomAD v4.1.

How common is CPD p.Pro1019Ser (c.3055C>T) in the general population?

CPD p.Pro1019Ser (c.3055C>T) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about CPD p.Pro1019Ser (c.3055C>T)?

AlphaMissense predicts likely benign (score 0.0968) — an in-silico prediction, not a clinical call.

CPD p.Pro1019Ser

c.3055C>T · rs2509722895 · VCV3076605

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0968 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.0968	likely benign
REVEL	0.076	moderately benign-leaning
SaProt	LLR -6.73	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 3.4	GERP 1, phastCons 1
Regional constraint	o/e 0.71	unconstrained · MANE · 19 kb · p 2e-11 · regional, not allelic
Overall
CADD	20.6	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

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: CPD
Protein: p.Pro1019Ser
Coding: c.3055C>T
MANE Select: NM_001304
dbSNP: rs2509722895
Type: single nucleotide variant
Location: chr17:30449734 (GRCh38)
Gene constraint: LOEUF 0.627 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 83.14 · 3 PDB
Residue 1019: the peptidase m14 3 domain

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

Similar variants

CPD p.Arg5= Benign ★★ same type
CPD p.Lys499Arg Benign ★★ same type
CPD p.Val677= Benign ★★ same type
CPD p.Ala122Val Uncertain significance ★ ⚠ same type
CPD p.Ala1263Thr Uncertain significance ★ ⚠ same type
CPD p.Ala157Val Uncertain significance ★ ⚠ same type
CPD p.Ala158Val Uncertain significance ★ ⚠ same type
CPD p.Ala46Val 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/cpd-p-pro1019ser (accessed [today's date]).

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