Is PALLD p.Pro648Ser (c.1942C>T) pathogenic?

PALLD p.Pro648Ser (c.1942C>T) is classified Uncertain significance in PALLD (ClinVar, Multiple submitters, 2 submitters; last evaluated 2024-04-10). Absent from gnomAD v4.1; Associated with pancreatic cancer, susceptibility to, 1.

What condition is associated with PALLD p.Pro648Ser (c.1942C>T)?

PALLD p.Pro648Ser (c.1942C>T) is associated with pancreatic cancer, susceptibility to, 1 (ClinVar).

How common is PALLD p.Pro648Ser (c.1942C>T) in the general population?

PALLD p.Pro648Ser (c.1942C>T) is absent from gnomAD v4.1 (gnomAD).

PALLD p.Pro648Ser

c.1942C>T · rs1784871346 · VCV1783073

Uncertain significance Multiple submitters

Classification

Uncertain significance

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

pancreatic cancer, susceptibility to, 1

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.356	indeterminate
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 7.7	GERP 2.1, phastCons 1
Regional constraint	o/e 0.99	unconstrained · MANE · 387 kb · p 0.73 · regional, not allelic
Overall
CADD	23.8	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: PALLD
Protein: p.Pro648Ser
Coding: c.1942C>T
MANE Select: NM_001166108
dbSNP: rs1784871346
Type: single nucleotide variant
Location: chr4:168711901 (GRCh38)
Gene constraint: LOEUF 0.644 · pLI <0.01 · ClinGen HI 0/3 (gnomAD)
Structure: AlphaFold pLDDT 54.74 · 2 PDB
Residue 648: the 'disordered' region; the 'interaction with lasp1' region

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

Disease context

pancreatic cancer, susceptibility to, 1 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

PALLD p.Pro648= Likely benign ★ same residue
PALLD c.*108C>T Uncertain significance ★★ same condition
PALLD p.Arg272Gln Uncertain significance ★★ same condition
PALLD p.Arg287Gln Uncertain significance ★★ same condition
PALLD p.Arg379Gly Uncertain significance ★★ same condition
PALLD p.Arg524Ile Uncertain significance ★★ same condition
PALLD p.Arg686Gln Uncertain significance ★★ same condition
PALLD p.Arg876His Uncertain significance ★★ same condition

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/palld-p-pro648ser (accessed [today's date]).

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