Is PALLD p.Pro902Ser (c.2704C>T) pathogenic?

PALLD p.Pro902Ser (c.2704C>T) is classified Uncertain significance in PALLD (ClinVar, Single submitter, 1 submitter; last evaluated 2022-09-28). Ultra-rare (popmax 0.0107%, afr); Associated with pancreatic adenocarcinoma.

What condition is associated with PALLD p.Pro902Ser (c.2704C>T)?

PALLD p.Pro902Ser (c.2704C>T) is associated with pancreatic adenocarcinoma (ClinVar).

How common is PALLD p.Pro902Ser (c.2704C>T) in the general population?

PALLD p.Pro902Ser (c.2704C>T) is ultra-rare (popmax 0.0107%, afr) (gnomAD).

PALLD p.Pro902Ser

c.2704C>T · rs114673468 · VCV1375172

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0107%, afr)

Conditions

pancreatic adenocarcinoma

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.134	moderately benign-leaning
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP 3.3	GERP 2, phastCons 1
Regional constraint	o/e 0.78	unconstrained · MANE · 27 kb · p 5.4e-06 · regional, not allelic
Overall
CADD	24.1	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0107% African / African-American · 8/74,732 alleles

Filtering AF 0.00529% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00381%

Overall 0.000812% 13/1,600,892 alleles · ultra-rare exomes 8/1,448,576 · genomes 5/152,316 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.0107%	9,342
Remaining individualsnot grpmax-eligible	0.00645%	15,500
Admixed American	0.00167%	60,016

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.Pro902Ser
Coding: c.2704C>T
MANE Select: NM_001166108
dbSNP: rs114673468
Type: single nucleotide variant
Location: chr4:168914008 (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-pro902ser (accessed [today's date]).

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