Is PELP1 p.Pro640= (c.1920C>T) pathogenic?

PELP1 p.Pro640= (c.1920C>T) is classified Likely benign in PELP1 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-12-25). Absent from gnomAD v4.1.

How common is PELP1 p.Pro640= (c.1920C>T) in the general population?

PELP1 p.Pro640= (c.1920C>T) is absent from gnomAD v4.1 (gnomAD).

PELP1 p.Pro640=

c.1920C>T · VCV3887777

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 1.8	GERP -0.1, phastCons 0.94
Overall
CADD	3.11	PHRED · no single calibrated threshold — expert panels disagree

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: PELP1
Protein: p.Pro640=
Coding: c.1920C>T
MANE Select: NM_014389
Type: single nucleotide variant
Location: chr17:4673071 (GRCh38)
Gene constraint: LOEUF 0.567 · pLI 0.18 (gnomAD)
Structure: AlphaFold pLDDT 64.18 · 7 PDB
Residue 640: the 'disordered' region

Full PELP1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

PELP1 c.1157+1G>A Uncertain significance ★ same type
PELP1 c.1275-2A>G Uncertain significance ★ same type
PELP1 c.25C>G Uncertain significance ★ same type
PELP1 c.421-1G>T Uncertain significance ★ same type
PELP1 c.56G>T Uncertain significance ★ same type
PELP1 c.86C>G Uncertain significance ★ same type
PELP1 p.Ala14Val Uncertain significance ★ ⚠ same type
PELP1 p.Ala376Val 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/pelp1-p-pro640 (accessed [today's date]).

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