Is PALLD p.Pro967= (c.2901C>T) pathogenic?

PALLD p.Pro967= (c.2901C>T) is classified Likely benign in PALLD (ClinVar, Multiple submitters, 2 submitters; last evaluated 2025-07-28). Ultra-rare (popmax 0.0135%, amr); Associated with pancreatic adenocarcinoma.

What condition is associated with PALLD p.Pro967= (c.2901C>T)?

PALLD p.Pro967= (c.2901C>T) is associated with pancreatic adenocarcinoma (ClinVar).

How common is PALLD p.Pro967= (c.2901C>T) in the general population?

PALLD p.Pro967= (c.2901C>T) is ultra-rare (popmax 0.0135%, amr) (gnomAD).

PALLD p.Pro967=

c.2901C>T · rs533269596 · VCV1130413

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

ultra-rare (popmax 0.0135%, amr)

Conditions

pancreatic adenocarcinoma

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.03	moderately benign-leaning
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP -2	GERP -4.7
Overall
CADD	5.197	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0135% Admixed American · 8/59,286 alleles

Filtering AF 0.00668% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00487%

Overall 0.00118% 19/1,609,098 alleles · ultra-rare

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.0135%	7,411
Remaining individualsnot grpmax-eligible	0.0016%	62,356
African / African-American	0.00137%	73,240
South Asian	0.0011%	90,534
European (non-Finnish)	0.000679%	147,384

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: PALLD
Protein: p.Pro967=
Coding: c.2901C>T
MANE Select: NM_032783 · reported on NM_001166108
dbSNP: rs533269596
Type: single nucleotide variant
Location: chr4:168921584 (GRCh38)

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

Disease context

pancreatic adenocarcinoma — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

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-pro967 (accessed [today's date]).

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