Is CPED1 p.Pro628Ser (c.1882C>T) pathogenic?

CPED1 p.Pro628Ser (c.1882C>T) is classified Uncertain significance in CPED1 (ClinVar, Single submitter, 1 submitter; last evaluated 2021-08-10). AlphaMissense: likely benign (0.1305); Absent from gnomAD v4.1.

How common is CPED1 p.Pro628Ser (c.1882C>T) in the general population?

CPED1 p.Pro628Ser (c.1882C>T) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about CPED1 p.Pro628Ser (c.1882C>T)?

AlphaMissense predicts likely benign (score 0.1305) — an in-silico prediction, not a clinical call.

CPED1 p.Pro628Ser

c.1882C>T · rs2485461946 · VCV2242878

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1305 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.1305	likely benign
REVEL	0.144	moderately benign-leaning
SaProt	LLR -3.75	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 4.9	GERP 3.8, phastCons 1
Regional constraint	o/e 1.00	unconstrained · MANE · 306 kb · p 0.91 · regional, not allelic
Overall
CADD	23.9	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

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: CPED1
Protein: p.Pro628Ser
Coding: c.1882C>T
MANE Select: NM_024913
dbSNP: rs2485461946
Type: single nucleotide variant
Location: chr7:121141009 (GRCh38)
Gene constraint: LOEUF 1.142 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 73.08

Full CPED1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CPED1 c.2634-3C>A Benign ★★ same type
CPED1 p.Gly140= Benign ★★ same type
CPED1 p.Lys949Thr Benign ★★ same type
CPED1 p.Thr293= Benign ★★ same type
CPED1 p.Ala43Pro Uncertain significance ★ ⚠ same type
CPED1 p.Ala44Gly Uncertain significance ★ ⚠ same type
CPED1 p.Ala652Val Uncertain significance ★ ⚠ same type
CPED1 p.Arg1018Ser 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/cped1-p-pro628ser (accessed [today's date]).

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